Methods and systems for determining spatial patterns of biological targets in a sample

ABSTRACT

The present disclosure provides methods and assay systems for use in spatially encoded biological assays, including assays to determine a spatial pattern of abundance, expression, and/or activity of one or more biological targets across multiple sites in a sample. In particular, the biological targets comprise proteins, and the methods and assay systems do not depend on imaging techniques for the spatial information of the targets. The present disclosure provides methods and assay systems capable of high levels of multiplexing where reagents are provided to a biological sample in order to address tag the sites to which reagents are delivered; instrumentation capable of controlled delivery of reagents; and a decoding scheme providing a readout that is digital in nature.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/180,356, filed on Feb. 19, 2021, which is a continuation of U.S.patent application Ser. No. 16/986,922, filed on Aug. 6, 2020, nowissued U.S. Pat. No. 10,927,403, which is a continuation of U.S. patentapplication Ser. No. 16/596,200, filed on Oct. 8, 2019, now issued U.S.Pat. No. 10,774,372, which is a continuation of U.S. patent applicationSer. No. 15/831,158, filed on Dec. 4, 2017, which is a continuation ofU.S. patent application Ser. No. 14/900,604, filed Dec. 21, 2015, nowissued U.S. Pat. No. 9,879,313, which is a U.S. national phaseapplication of International Application No. PCT/US2014/044196, filedJun. 25, 2014, which claims benefit of priority to U.S. ProvisionalPatent Application Ser. No. 61/839,320, filed Jun. 25, 2013, entitled“Spatially encoded biological assays using a microfluidic device,” andU.S. Provisional Patent Application Ser. No. 61/839,313, filed Jun. 25,2013, entitled “Methods and systems for determining spatial patterns ofbiological targets in a sample,” the disclosures of which areincorporated by reference herein in their entireties. In someembodiments, this application is related to U.S. patent application Ser.No. 14/900,602, filed Dec. 21, 2015, now issued U.S. Pat. No. 9,868,979,which is a U.S. national phase application of International ApplicationNo. PCT/US2014/044191, filed Jun. 25, 2014, entitled “Spatially encodedbiological assays using a microfluidic device,” the disclosure of whichis incorporated by reference herein in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with the support by the Department of Health andHuman Services, National Institute of General Medical Sciences GrantNumber R43GM096706, and National Human Genome Research Institute GrantNumber R43HG006223. The U.S. government may have certain rights in thisinvention.

TECHNICAL FIELD

The present disclosure generally relates to assays of biologicalmolecules, and in particular, to methods, compositions, and assaysystems for determining spatial patterns of abundance, expression,and/or activity of one or more biological targets across multiple sitesin a sample.

BACKGROUND

In the following discussion, certain articles and methods are describedfor background and introductory purposes. Nothing contained herein is tobe construed as an “admission” of prior art. Applicant expresslyreserves the right to demonstrate, where appropriate, that the articlesand methods referenced herein do not constitute prior art under theapplicable statutory provisions.

Comprehensive gene expression analysis and protein analysis have beenuseful tools in understanding mechanisms of biology. Use of these toolshas allowed the identification of genes and proteins involved indevelopment and in various diseases such as cancer and autoimmunedisease. Conventional methods such as in situ hybridization and othermultiplexed detection of different transcripts have revealed spatialpatterns of gene expression and have helped shed light on the molecularbasis of development and disease. Other technologies that have enabledthe quantitative analysis of many RNA sequences per sample includemicroarrays (see Shi et al., Nature Biotechnology, 24(9):1151-61 (2006);and Slonim and Yanai, Plos Computational Biology, 5(10):e1000543(2009)); serial analysis of gene expression (SAGE) (see Velculescu etal., Science, 270(5235):484-87 (1995)); high-throughput implementationsof qPCR (see Spurgeon et al., Plos ONE, 3(2):e1662 (2008)); in situ PCR(see Nuovo, Genome Res., 4:151-67 (1995)); and RNA-Seq (see Mortazavi etal., Nature Methods, 5(7):621-8 (2008)). As useful as these methods are,however, they do not enable simultaneous measurement of the expressionof many genes or the presence and/or activity of multiple proteins atmany spatial locations in a sample.

Laser capture microdissection has permitted the analysis of many genesat a small number of locations, but it is very expensive, laborious, anddoes not scale well. Certain PCR assays in a 2D format preserve spatialinformation (see Armani et al., Lab on a Chip, 9(24):3526-34 (2009)),but these methods have low spatial resolution because they rely onphysically transferring tissues into wells, which also prevents randomaccess to tissue samples and high levels of multiplexing.

At present, there is a need to analyze at high resolution the spatialexpression patterns of large numbers of genes, proteins, or otherbiologically active molecules simultaneously. There is also a need forreproducible, high-resolution spatial maps of biological molecules intissues. The present disclosure addresses these needs.

SUMMARY

In one aspect, disclosed herein is a method of determining a spatialpattern of abundance, expression, and/or activity of one or morebiological targets across multiple sites in a sample, comprising:

delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises: (1) atarget-binding moiety capable of binding to the probe's correspondingbiological target; (2) an address tag that identifies each of themultiple sites to which the probe is delivered; and (3) an identity tagthat identifies the probe's corresponding biological target ortarget-binding moiety;

allowing each probe to bind to its corresponding biological target inthe sample;

analyzing the probe bound to the one or more biological targets, theanalysis comprising: (1) determining abundance, expression, and/oractivity of each of the one or more biological targets by assessing theamount of the probe bound to the biological target; and (2) determiningthe identities of the identity tag and the address tag of the probe; and

determining a spatial pattern of abundance, expression, and/or activityof the one or more biological targets across the multiple sites in thesample based on the analysis. In some embodiments, the method does notdepend on an imaging technique for determining spatial information ofthe one or more biological targets in the sample. In one embodiment,analysis of the probe bound to the one or more biological targets can bedone by sequencing, wherein the amount of a sequencing product indicatesabundance, expression, and/or activity of each of the one or morebiological targets, and the sequencing product may comprise all or aportion of the address tag sequence and all or a portion of the identitytag sequence.

In another aspect, disclosed herein is a method of determining a spatialpattern of abundance, expression, and/or activity of one or morebiological targets across multiple sites in a sample, comprising:

delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises: (1) atarget-binding moiety capable of binding to the probe's correspondingbiological target; and (2) an identity tag that identifies the probe'scorresponding biological target or target-binding moiety;

allowing each probe to bind to its corresponding biological target inthe sample;

delivering an address tag to each of the multiple sites in the sample,wherein the address tag is to be coupled to the probe bound to thebiological target and identifies the site to which the address tag isdelivered;

analyzing the probe/address tag conjugate bound to the one or morebiological targets, the analysis comprising: (1) determining abundance,expression, and/or activity of each of the one or more biologicaltargets by assessing the amount of the probe/address tag conjugate boundto the biological target; and (2) determining the identities of theidentity tag and the address tag of the probe/address tag conjugate; and

determining a spatial pattern of abundance, expression, and/or activityof the one or more biological targets across the multiple sites in thesample based on the analysis. In some embodiments, the method does notdepend on an imaging technique for determining spatial information ofthe one or more biological targets in the sample. In one embodiment, theprobe/address tag conjugate bound to the one or more biological targetsmay be analyzed by sequencing, wherein the amount of a sequencingproduct indicates abundance, expression, and/or activity of each of theone or more biological targets, and the sequencing product may compriseall or a portion of the address tag sequence and all or a portion of theidentity tag sequence.

In any of the preceding embodiments or combinations thereof, the one ormore biological targets can be non-nucleic acid molecules. In any of thepreceding embodiments, the one or more biological targets may comprise aprotein, a lipid, a carbohydrate, or any combination thereof. In any ofthe preceding embodiments, there can be at least two address tags thatidentify each of the multiple sites in the sample.

In any of the preceding embodiments, the spatial patterns of abundance,expression, and/or activity of multiple biological targets can bedetermined in parallel, and the address tag or combination of addresstags may be the same for each of the multiple biological targets at agiven site of the multiple sites in the sample. In any of the precedingembodiments, the analyzing step may be performed in parallel in the samereaction run.

In any of the preceding embodiments or combinations thereof, the one ormore biological targets may include at least one known marker for thesample, for example, a tissue-specific marker, a cell type marker, acell lineage marker, a cell morphology marker, a cell cycle marker, acell death marker, a developmental stage marker, a stem cell orprogenitor cell marker, a marker for a differentiated state, anepigenetic marker, a physiological or pathophysiological marker, amarker for a transformed state, a cancer marker, or any combinationthereof.

In yet another embodiment, provided herein is a method of determining aspatial pattern of abundance, expression, and/or activity of a targetprotein across multiple sites in a sample, comprising:

delivering a probe for a target protein to multiple sites in a sample,wherein the probe comprises: (1) a target-binding moiety capable ofbinding to the target protein; (2) a first address tag that identifieseach of the multiple sites to which the probe is delivered; and (3) anidentity tag that identifies the target protein or the target-bindingmoiety;

allowing the probe to bind to the target protein in the sample;

analyzing the probe bound to the target protein, the analysiscomprising: (1) determining abundance, expression, and/or activity ofthe target protein by assessing the amount of the probe bound to thetarget protein; and (2) determining the identities of the identity tagand the first address tag of the probe for the target protein; and

determining a spatial pattern of abundance, expression, and/or activityof the target protein across the multiple sites in the sample based onthe analysis.

In any of the preceding embodiments, the method may further comprise:

delivering a probe for a target polynucleotide to each of the multiplesites in the sample, wherein the probe for the target polynucleotidecomprises: (1) a sequence that hybridizes to and identifies the targetpolynucleotide; (2) a second address tag that identifies each of themultiple sites to which the probe for the target polynucleotide isdelivered;

allowing the probe for the target polynucleotide to bind to the targetpolynucleotide in the sample;

analyzing the probe bound to the target polynucleotide, the analysiscomprising: (1) determining abundance, expression, and/or activity ofthe target polynucleotide by assessing the amount of the probe bound tothe target polynucleotide; and (2) determining the identities of thesequence that hybridizes to and identifies the target polynucleotide andthe second address tag of the probe for the target polynucleotide; and

determining a spatial pattern of abundance, expression, and/or activityof the target polynucleotide across the multiple sites in the samplebased on the analysis of the probe bound to the target polynucleotide ateach of the multiple sites in the sample.

In another aspect, disclosed herein is a method of determining a spatialpattern of abundance, expression, and/or activity of a target proteinacross multiple sites in a sample, comprising:

delivering a probe for a target protein to multiple sites in the sample,wherein the probe comprises: (1) a target-binding moiety capable ofbinding to the target protein; and (2) an identity tag that identifiesthe target protein or the protein-binding moiety;

allowing the probe to bind to the target protein in the sample;

delivering a first address tag to each of the multiple sites in thesample, wherein the first address tag is to be coupled to the probebound to the target protein and identifies the site to which it isdelivered;

analyzing the probe/first address tag conjugate bound to the targetprotein, the analysis comprising: (1) determining abundance, expression,and/or activity of the target protein by assessing the amount of theprobe/first address tag conjugate bound to the target protein; and (2)determining the identities of the identity tag and the first address tagof the probe/first address tag conjugate; and

determining a spatial pattern of abundance, expression, and/or activityof the target protein across the multiple sites in the sample based onthe analysis.

In any of the preceding embodiment, the method may further comprise:

delivering a probe for a target polynucleotide to each of the multiplesites in the sample, wherein the probe for the target polynucleotidecomprises a sequence that hybridizes to and identifies the targetpolynucleotide;

allowing the probe for the target polynucleotide to bind to the targetpolynucleotide in the sample;

delivering a second address tag to each of the multiple sites in thesample, wherein the second address tag is to be coupled to the probebound to the target polynucleotide and identifies the site to which itis delivered;

analyzing the probe/second address tag conjugate bound to the targetpolynucleotide, the analysis comprising: (1) determining abundance,expression, and/or activity of the target polynucleotide by assessingthe amount of the probe/second address tag conjugate bound to the targetpolynucleotide; and (2) determining the identities of the sequence thathybridizes to and identifies the target polynucleotide and the secondaddress tag of the probe/second address tag conjugate; and

determining a spatial pattern of abundance, expression, and/or activityof the target polynucleotide across the multiple sites in the samplebased on the analysis of the probe/second address tag conjugate bound tothe target polynucleotide at each of the multiple sites in the sample.

In one embodiment, the target polynucleotide or the complement thereofmay encode all or a portion of the target protein. In some embodiments,the step of analyzing the probe or probe/first address tag conjugatebound to the target protein and the step of analyzing the probe orprobe/second address tag conjugate bound to the target polynucleotidemay be performed in parallel in the same reaction run. In other aspects,the first address tag and the second address tag may be the same for agiven site of the multiple sites in the sample. In yet other aspects,the first address tag and the second address tag can be different for agiven site of the multiple sites in the sample. In any of the precedingembodiments, the method may further comprise associating abundance,expression, and/or activity of the target protein to abundance,expression, and/or activity of the target polynucleotide at each of themultiple sites in the sample.

In any of the preceding embodiments or any combinations thereof, thebiological target or the target protein may comprise an enzyme activity.In certain aspects, the target-binding moiety of the probe in any of thepreceding embodiments may comprise an antibody or an antigen bindingfragment thereof, an aptamer, a small molecule, an enzyme substrate, aputative enzyme substrate, an affinity capture agent, or a combinationthereof.

In any of the preceding embodiments or any combinations thereof, thetarget-binding moiety is conjugated to a polynucleotide comprising theidentity tag. In any of the preceding embodiments, the target-bindingmoiety may be conjugated to a polynucleotide capable of specificallyhybridizing to a polynucleotide comprising the identity tag. In certainaspects, the probe may comprise a multiplicity of target-bindingmoieties capable of binding to the same domain or different domains ofthe target, or capable of binding to different targets.

In any of the preceding embodiments or any combinations thereof, thesample can be a biological sample selected from the group consisting ofa freshly isolated sample, a fixed sample, a frozen sample, an embeddedsample, a processed sample, or a combination thereof.

In any of the preceding embodiments or any combinations thereof, therecan be two address tags that identify each of the multiple sites in thesample. In certain aspects, two probes for each target can be deliveredto the sample.

In any of the preceding embodiments or any combinations thereof, theaddress tag may comprise an oligonucleotide. In another aspect, theidentity tag of any of the preceding embodiments may comprise anoligonucleotide.

In any of the preceding embodiments or any combinations thereof, theanalyzing step may be performed by nucleic acid sequencing. In oneaspect, the analyzing step can be performed by high-throughput digitalnucleic acid sequencing.

In any of the preceding embodiments or any combinations thereof, theproduct of the number of the target(s) being assayed and the number ofthe multiple sites being assayed in the sample can be greater than 20,greater than 50, greater than 75, greater than 100, greater than 1,000,greater than 10,000, greater than 100,000, or greater than 1,000,000.

In any of the preceding embodiments or any combinations thereof, atleast one hundred thousand, at least five hundred thousand, or at leastone million probes or probe/address tag conjugates bound to thetarget(s) may be analyzed in parallel.

In any of the preceding embodiments or any combinations thereof,software programmed hardware may perform at least two steps of thedelivering step(s), the analyzing step(s) and the determining step(s).In any of the preceding embodiments or any combinations thereof, one ormore microfluidic devices may be used to perform the delivering step(s).

In any of the preceding embodiments or any combinations thereof, a knownpercentage of the probe for the biological target, the probe for thetarget protein, or the probe for the target polynucleotide can be anattenuator probe. In one aspect, the attenuator probe may limitproduction of an amplifiable product. For example, an attenuator probemay compete with an active probe for binding to the target. While anactive probe can lead to the generation of an amplifiable product fromthe target, an attenuator probe does not or has reduced ability ingenerating an amplifiable product. In one embodiment where a nucleicacid probe is used, the attenuator probe can lack a 5′ phosphate.

In any of the preceding embodiments or any combinations thereof, theaddress tag may be coupled to the probe by ligation, by extension, byligation following extension, or any combination thereof.

In any of the preceding embodiments or any combinations thereof, themethod may further comprise constructing a 3-dimensional pattern ofabundance, expression, and/or activity of each target from spatialpatterns of abundance, expression, and/or activity of each target ofmultiple samples. In one aspect, the multiple samples can be consecutivetissue sections of a 3-dimensional tissue sample.

In yet another aspect, provided herein is a system for determining aspatial pattern of abundance, expression, and/or activity of one or morebiological targets across multiple sites in a sample, comprising:

a first module for delivering a probe for each of one or more biologicaltargets to multiple sites in a sample, wherein each probe comprises: (1)a target-binding moiety capable of binding to the probe's correspondingbiological target; and (2) an identity tag that identifies the probe'scorresponding biological target or target-binding moiety;

a second module for delivering an address tag to each of the multiplesites in the sample, wherein the address tag is to be coupled to theprobe bound to the biological target and identifies the site to whichthe address tag is delivered;

a third module for analyzing the probe/address tag conjugate bound tothe one or more biological targets, the analysis comprising: (1)determining abundance, expression, and/or activity of the one or morebiological targets by assessing the amount of the probe/address tagconjugate bound to the biological target; and (2) determining theidentities of the identity tag and the address tag of the probe/addresstag conjugate; and

a fourth module for determining a spatial pattern of abundance,expression, and/or activity of the one or more biological targets acrossthe multiple sites in the sample based on the analysis. In one aspect,the system does not depend on an imaging technique for determiningspatial information of the one or more biological targets in the sample.

In one embodiment, the second module may comprise one or moremicrofluidic devices for delivering the address tags. In one aspect, theone or more microfluidic devices may comprise a first set of multipleaddressing channels, each delivering a different first address tag tothe sample. In one embodiment, the one or more microfluidic devices mayfurther comprise a second set of multiple addressing channels, eachdelivering a different second address tag to the sample. In one aspect,the multiple sites in the sample can be chosen by the first and secondset of multiple addressing channels cooperatively delivering the firstaddress tags and the second address tags, respectively, to each of themultiple sites, each site identified by a different combination of firstand second address tags.

In another embodiment, disclosed herein is a method comprising:delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises atarget-binding moiety capable of binding to the probe's correspondingbiological target; allowing each probe to bind to its correspondingbiological target in the sample; delivering at least one adaptor to themultiple sites in the sample, wherein the at least one adaptorspecifically binds to the probe and comprises an address tag thatidentifies each of the multiple sites to which the at least one adaptoris delivered, wherein the probe and/or the adaptor comprises an identitytag that identifies the probe's and/or adaptor's correspondingbiological target or target-binding moiety; analyzing the at least oneadaptor and the probe bound to the one or more biological targets, theanalysis comprising: (1) determining abundance, expression, and/oractivity of each of the one or more biological targets by assessing theamount of at least one adaptor bound to the probe bound to thebiological target; and (2) determining the identities of the identitytag, and the address tag of the at least one adaptor; and determining aspatial pattern of abundance and/or activity of the one or morebiological targets across the multiple sites in the sample based on theanalysis. In one aspect, the method does not depend on an imagingtechnique for determining spatial information of the one or morebiological targets in the sample.

In another embodiment, disclosed herein is a method comprising:delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises atarget-binding moiety capable of binding to the probe's correspondingbiological target; allowing each probe to bind to its correspondingbiological target in the sample; delivering at least one adaptor to themultiple sites in the sample, wherein the at least one adaptorspecifically binds to the probe and comprises an address tag thatidentifies each of the multiple sites to which the at least one adaptoris delivered, wherein the probe and/or the adaptor comprises an identitytag that identifies the probe's and/or adaptor's correspondingbiological target or target-binding moiety; analyzing the at least oneadaptor and the probe bound to the one or more biological targets bysequencing, wherein the amount of a sequencing product indicatesabundance, expression, and/or activity of each of the one or morebiological targets, the sequencing product comprising all or a portionof the address tag sequence and all or a portion of the identity tagsequence; and determining a spatial pattern of abundance, expression,and/or activity of the one or more biological targets across themultiple sites in the sample based on the analysis. In one aspect, themethod does not depend on an imaging technique for determining spatialinformation of the one or more biological targets in the sample.

In yet another embodiment, provided herein is a method comprising:delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises atarget-binding moiety capable of binding to the probe's correspondingbiological target; allowing each probe to bind to its correspondingbiological target in the sample; delivering at least one adaptor to themultiple sites in the sample, wherein the at least one adaptorspecifically binds to the probe, wherein the probe and/or the adaptorcomprises an identity tag that identifies the probe's and/or adaptor'scorresponding biological target or target-binding moiety; delivering anaddress tag to each of the multiple sites in the sample, wherein theaddress tag is to be coupled to the at least one adaptor bound to theprobe bound to the biological target and identifies the site to whichthe address tag is delivered; analyzing the adaptor/address tagconjugate, the analysis comprising: (1) determining abundance,expression, and/or activity of each of the one or more biologicaltargets by assessing the amount of the adaptor/address tag conjugatebound to the probe bound to the biological target; and (2) determiningthe identities of the identity tag, and the address tag of theadaptor/address tag conjugate; and determining a spatial pattern ofabundance, expression, and/or activity of the one or more biologicaltargets across the multiple sites in the sample based on the analysis.In one embodiment, the method does not depend on an imaging techniquefor determining spatial information of the one or more biologicaltargets in the sample.

In still another embodiment, provided herein is a method comprising:delivering a probe for each of one or more biological targets tomultiple sites in a sample, wherein each probe comprises atarget-binding moiety capable of binding to the probe's correspondingbiological target; allowing each probe to bind to its correspondingbiological target in the sample; delivering at least one adaptor to themultiple sites in the sample, wherein the at least one adaptorspecifically binds to the probe, wherein the probe and/or the adaptorcomprises an identity tag that identifies the probe's and/or adaptor'scorresponding biological target or target-binding moiety; delivering anaddress tag to each of the multiple sites in the sample, wherein theaddress tag is to be coupled to the at least one adaptor bound to theprobe bound to the biological target and identifies the site to whichthe address tag is delivered; analyzing the adaptor/address tagconjugate by sequencing, wherein the amount of a sequencing productindicates abundance, expression, and/or activity of each of the one ormore biological targets, the sequencing product comprising all or aportion of the address tag sequence and all or a portion of the identitytag sequence; and determining a spatial pattern of abundance,expression, and/or activity of the one or more biological targets acrossthe multiple sites in the sample based on the analysis. In one aspect,the method does not depend on an imaging technique for determiningspatial information of the one or more biological targets in the sample.

In any of the preceding embodiments, at least two adaptors can bedelivered to each of the multiple sites in the sample, wherein the atleast two adaptors each specifically binds to one probe thatspecifically binds to the biological target. In one aspect, the at leasttwo adaptors are joined, for example, by ligation using a portion of theprobe sequence as a splint.

In any of the preceding embodiments, the probe for each of the one ormore biological targets can comprise an affinity agent for thebiological target and an oligonucleotide, and the adaptor can comprisean oligonucleotide.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a flow chart illustrating exemplary steps of a method ofdetermining a spatial pattern of abundance, expression, and/or activityof one or more biological targets across multiple sites in a sample,according to an embodiment of the present disclosure.

FIG. 2 is a flow chart illustrating exemplary steps of a method ofdetermining a spatial pattern of abundance, expression, and/or activityof one or more biological targets across multiple sites in a sample,according to an embodiment of the present disclosure.

FIG. 3 illustrates a combinatorial addressing scheme, according to oneembodiment of the present disclosure.

FIGS. 4A-4D illustrate combinatorial addressing schemes applied to asample, according to embodiments of the present disclosure.

FIG. 5 illustrates a combinatorial addressing scheme applied to asample, according to one embodiment of the present disclosure.

FIGS. 6A-6E illustrate multiplexable protein detection assays withcombinatorial addressing schemes applied to a sample, according toembodiments of the present disclosure.

FIGS. 7A-7C illustrate exemplary antibody-DNA conjugate configurations,according to certain embodiments of the present disclosure.

FIGS. 8A and 8B illustrate sequential address tagging schemes, accordingto embodiments of the present disclosure.

FIGS. 9A-9C illustrate a microfluidic addressing device, according toone embodiment of the present disclosure.

FIGS. 10A-10C provide an immunofluorescence image (FIG. 10A) andrepresentative expression maps (FIGS. 10B and C) generated according tosome embodiments of the present disclosure.

FIGS. 11A and 11B illustrate a method for reducing random errors duringthe sequencing step (FIG. 11A), and exemplary configurations of probeswith integrated X and Y address tags and variable tag region z (FIG.11B), according to some embodiments of the present disclosure.

DETAILED DESCRIPTION

A detailed description of one or more embodiments of the claimed subjectmatter is provided below along with accompanying figures that illustratethe principles of the claimed subject matter. The claimed subject matteris described in connection with such embodiments, but is not limited toany embodiment. It is to be understood that the claimed subject mattermay be embodied in various forms, and encompasses numerous alternatives,modifications and equivalents. Therefore, specific details disclosedherein are not to be interpreted as limiting, but rather as a basis forthe claims and as a representative basis for teaching one skilled in theart to employ the claimed subject matter in virtually any appropriatelydetailed system, structure or manner. Numerous specific details are setforth in the following description in order to provide a thoroughunderstanding of the present disclosure. These details are provided forthe purpose of example and the claimed subject matter may be practicedaccording to the claims without some or all of these specific details.It is to be understood that other embodiments can be used and structuralchanges can be made without departing from the scope of the claimedsubject matter. For the purpose of clarity, technical material that isknown in the technical fields related to the claimed subject matter hasnot been described in detail so that the claimed subject matter is notunnecessarily obscured.

Unless defined otherwise, all terms of art, notations and othertechnical and scientific terms or terminology used herein are intendedto have the same meaning as is commonly understood by one of ordinaryskill in the art to which the claimed subject matter pertains. In somecases, terms with commonly understood meanings are defined herein forclarity and/or for ready reference, and the inclusion of suchdefinitions herein should not necessarily be construed to represent asubstantial difference over what is generally understood in the art.Many of the techniques and procedures described or referenced herein arewell understood and commonly employed using conventional methodology bythose skilled in the art.

All publications, including patent documents, scientific articles anddatabases, referred to in this application and the bibliography andattachments are incorporated by reference in their entirety for allpurposes to the same extent as if each individual publication wereindividually incorporated by reference. If a definition set forth hereinis contrary to or otherwise inconsistent with a definition set forth inthe patents, applications, published applications and other publicationsthat are herein incorporated by reference, the definition set forthherein prevails over the definition that is incorporated herein byreference.

The practice of the provided embodiments will employ, unless otherwiseindicated, conventional techniques and descriptions of organicchemistry, polymer technology, molecular biology (including recombinanttechniques), cell biology, biochemistry, and sequencing technology,which are within the skill of those who practice in the art. Suchconventional techniques include polymer array synthesis, hybridizationand ligation of polynucleotides, and detection of hybridization using alabel. Specific illustrations of suitable techniques can be had byreference to the examples herein. However, other equivalent conventionalprocedures can, of course, also be used. Such conventional techniquesand descriptions can be found in standard laboratory manuals such asGreen, et al., Eds., Genome Analysis: A Laboratory Manual Series (Vols.I-IV) (1999); Weiner, Gabriel, Stephens, Eds., Genetic Variation: ALaboratory Manual (2007); Dieffenbach, Dveksler, Eds., PCR Primer: ALaboratory Manual (2003); Bowtell and Sambrook, DNA Microarrays: AMolecular Cloning Manual (2003); Mount, Bioinformatics: Sequence andGenome Anazvsis (2004); Sambrook and Russell, Condensed Protocols fromMolecular Cloning: A Laboratory Manual (2006); and Sambrook and Russell,Molecular Cloning: A Laboratory Manual (2002) (all from Cold SpringHarbor Laboratory Press); Ausubel et al. eds., Current Protocols inMolecular Biology (1987); T. Brown ed., Essential Molecular Biology(1991), IRL Press; Goeddel ed., Gene Expression Technology (1991),Academic Press; A. Bothwell et al. eds., Methods for Cloning andAnalysis of Eukaryotic Genes (1990), Bartlett Publ.; M. Kriegler, GeneTransfer and Expression (1990), Stockton Press; R. Wu et al. eds.,Recombinant DNA Methodology (1989), Academic Press; M. McPherson et al.,PCR: A Practical Approach (1991), IRL Press at Oxford University Press;Stryer, Biochemistry (4th Ed.) (1995), W. H. Freeman, New York N.Y.;Gait, Oligonucleotide Synthesis: A Practical Approach (2002), IRL Press,London; Nelson and Cox, Lehninger, Principles of Biochemistry (2000) 3rdEd., W. H. Freeman Pub., New York, N.Y.; Berg, et al., Biochemistry(2002) 5th Ed., W. H. Freeman Pub., New York, N.Y.; D. Weir & C.Blackwell, eds., Handbook of Experimental Immunology (1996),Wiley-Blackwell; A. Abbas et al., Cellular and Molecular Immunology(1991, 1994), W. B. Saunders Co.; and J. Coligan et al. eds., CurrentProtocols in Immunology (1991), all of which are herein incorporated intheir entirety by reference for all purposes.

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural referents unless the context clearly dictatesotherwise. For example, “a” or “an” means “at least one” or “one ormore.” Thus, reference to “a biological target” refers to one or morebiological targets, and reference to “the method” includes reference toequivalent steps and methods disclosed herein and/or known to thoseskilled in the art, and so forth.

Throughout this disclosure, various aspects of the claimed subjectmatter are presented in a range format. It should be understood that thedescription in range format is merely for convenience and brevity andshould not be construed as an inflexible limitation on the scope of theclaimed subject matter. Accordingly, the description of a range shouldbe considered to have specifically disclosed all the possible sub-rangesas well as individual numerical values within that range. For example,where a range of values is provided, it is understood that eachintervening value, between the upper and lower limit of that range andany other stated or intervening value in that stated range isencompassed within the claimed subject matter. The upper and lowerlimits of these smaller ranges may independently be included in thesmaller ranges, and are also encompassed within the claimed subjectmatter, subject to any specifically excluded limit in the stated range.Where the stated range includes one or both of the limits, rangesexcluding either or both of those included limits are also included inthe claimed subject matter. This applies regardless of the breadth ofthe range.

As used herein, an “individual” can be any living organism, includinghumans and other mammals. A “subject” as used herein can be an organismto which the provided compositions, methods, kits, devices, and systemscan be administered or applied. In one embodiment, the subject can be amammal or a cell, a tissue, an organ or a part of the mammal. Mammalsinclude, but are not limited to, humans, and non-human animals,including farm animals, sport animals, rodents and pets.

As used herein, a “biological sample” can refer to any sample obtainedfrom a living or viral source or other source of macromolecules andbiomolecules, and includes any cell type or tissue of a subject fromwhich nucleic acid or protein or other macromolecule can be obtained.The biological sample can be a sample obtained directly from abiological source or a sample that is processed. For example, isolatednucleic acids that are amplified constitute a biological sample.Biological samples include, but are not limited to, body fluids, such asblood, plasma, serum, cerebrospinal fluid, synovial fluid, urine andsweat, tissue and organ samples from animals and plants and processedsamples derived therefrom.

As used herein, a “composition” can be any mixture of two or moreproducts or compounds. It may be a solution, a suspension, liquid,powder, a paste, aqueous, non-aqueous or any combination thereof.

The terms “polynucleotide,” “oligonucleotide,” “nucleic acid” and“nucleic acid molecule” are used interchangeably herein to refer to apolymeric form of nucleotides of any length, and may compriseribonucleotides, deoxyribonucleotides, analogs thereof, or mixturesthereof. This term refers only to the primary structure of the molecule.Thus, the term includes triple-, double- and single-strandeddeoxyribonucleic acid (“DNA”), as well as triple-, double- andsingle-stranded ribonucleic acid (“RNA”). It also includes modified, forexample by alkylation, and/or by capping, and unmodified forms of thepolynucleotide. More particularly, the terms “polynucleotide,”“oligonucleotide,” “nucleic acid” and “nucleic acid molecule” includepolydeoxyribonucleotides (containing 2-deoxy-D-ribose),polyribonucleotides (containing D-ribose), including tRNA, rRNA, hRNA,and mRNA, whether spliced or unspliced, any other type of polynucleotidewhich is an N-or C-glycoside of a purine or pyrimidine base, and otherpolymers containing normucleotidic backbones, for example, polyamide(e.g., peptide nucleic acids (“PNAs”)) and polymorpholino (commerciallyavailable from the Anti-Virals, Inc., Corvallis, Oreg., as Neugene)polymers, and other synthetic sequence-specific nucleic acid polymersproviding that the polymers contain nucleobases in a configuration whichallows for base pairing and base stacking, such as is found in DNA andRNA. Thus, these terms include, for example, 3′-deoxy-2′,5′-DNA,oligodeoxyribonucleotide N3′ to P5′ phosphoramidates,2′-O-alkyl-substituted RNA, hybrids between DNA and RNA or between PNAsand DNA or RNA, and also include known types of modifications, forexample, labels, alkylation, “caps,” substitution of one or more of thenucleotides with an analog, intemucleotide modifications such as, forexample, those with uncharged linkages (e.g., methyl phosphonates,phosphotriesters, phosphoramidates, carbamates, etc.), with negativelycharged linkages (e.g., phosphorothioates, phosphorodithioates, etc.),and with positively charged linkages (e.g., aminoalkylphosphoramidates,aminoalkylphosphotriesters), those containing pendant moieties, such as,for example, proteins (including enzymes (e.g. nucleases), toxins,antibodies, signal peptides, poly-L-lysine, etc.), those withintercalators (e.g., acridine, psoralen, etc.), those containingchelates (of, e.g., metals, radioactive metals, boron, oxidative metals,etc.), those containing alkylators, those with modified linkages (e.g.,alpha anomeric nucleic acids, etc.), as well as unmodified forms of thepolynucleotide or oligonucleotide. A nucleic acid generally will containphosphodiester bonds, although in some cases nucleic acid analogs may beincluded that have alternative backbones such as phosphoramidite,phosphorodithioate, or methylphophoroamidite linkages; or peptidenucleic acid backbones and linkages. Other analog nucleic acids includethose with bicyclic structures including locked nucleic acids, positivebackbones, non-ionic backbones and non-ribose backbones. Modificationsof the ribose-phosphate backbone may be done to increase the stabilityof the molecules; for example, PNA:DNA hybrids can exhibit higherstability in some environments. The terms “polynucleotide,”“oligonucleotide,” “nucleic acid” and “nucleic acid molecule” cancomprise any suitable length, such as at least 5, 6, 7, 8, 9, 10, 20,30, 40, 50, 100, 200, 300, 400, 500, 1,000 or more nucleotides.

It will be appreciated that, as used herein, the terms “nucleoside” and“nucleotide” will include those moieties which contain not only theknown purine and pyrimidine bases, but also other heterocyclic baseswhich have been modified. Such modifications include methylated purinesor pyrimidines, acylated purines or pyrimidines, or other heterocycles.Modified nucleosides or nucleotides can also include modifications onthe sugar moiety, e.g., wherein one or more of the hydroxyl groups arereplaced with halogen, aliphatic groups, or are functionalized asethers, amines, or the like. The term “nucleotidic unit” is intended toencompass nucleosides and nucleotides.

“Nucleic acid probe” refers to a structure comprising a polynucleotide,as defined above, that contains a nucleic acid sequence that can bind toa corresponding target. The polynucleotide regions of probes may becomposed of DNA, and/or RNA, and/or synthetic nucleotide analogs.

The terms “polypeptide”, “oligopeptide”, “peptide” and “protein” areused interchangeably herein to refer to polymers of amino acids of anylength, e.g., at least 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100, 200, 300,400, 500, 1,000 or more amino acids. The polymer may be linear orbranched, it may comprise modified amino acids, and it may beinterrupted by non-amino acids. The terms also encompass an amino acidpolymer that has been modified naturally or by intervention; forexample, disulfide bond formation, glycosylation, lipidation,acetylation, phosphorylation, or any other manipulation or modification,such as conjugation with a labeling component. Also included within thedefinition are, for example, polypeptides containing one or more analogsof an amino acid (including, for example, unnatural amino acids, etc.),as well as other modifications known in the art.

The terms “binding agent” and “target-binding moiety” as used herein mayrefer to any agent or any moiety thereof that specifically binds to abiological molecule of interest.

The biological targets or molecules to be detected can be any biologicalmolecules including but not limited to proteins, nucleic acids, lipids,carbohydrates, ions, or multicomponent complexes containing any of theabove. Examples of subcellular targets include organelles, e.g.,mitochondria, Golgi apparatus, endoplasmic reticulum, chloroplasts,endocytic vesicles, exocytic vesicles, vacuoles, lysosomes, etc.Exemplary nucleic acid targets can include genomic DNA of variousconformations (e.g., A-DNA, B-DNA, Z-DNA), mitochondria DNA (mtDNA),mRNA, tRNA, rRNA, hRNA, miRNA, and piRNA.

As used herein, “biological activity” may include the in vivo activitiesof a compound or physiological responses that result upon in vivoadministration of a compound, composition or other mixture. Biologicalactivity, thus, may encompass therapeutic effects and pharmaceuticalactivity of such compounds, compositions and mixtures. Biologicalactivities may be observed in vitro systems designed to test or use suchactivities.

The term “binding” can refer to an attractive interaction between twomolecules which results in a stable association in which the moleculesare in close proximity to each other. Molecular binding can beclassified into the following types: non-covalent, reversible covalentand irreversible covalent. Molecules that can participate in molecularbinding include proteins, nucleic acids, carbohydrates, lipids, andsmall organic molecules such as pharmaceutical compounds. Proteins thatform stable complexes with other molecules are often referred to asreceptors while their binding partners are called ligands. Nucleic acidscan also form stable complex with themselves or others, for example,DNA-protein complex, DNA-DNA complex, DNA-RNA complex.

As used herein, the term “specific binding” refers to the specificity ofa binder, e.g., an antibody, such that it preferentially binds to atarget, such as a polypeptide antigen. When referring to a bindingpartner (e.g., protein, nucleic acid, antibody or other affinity captureagent, etc.), “specific binding” can include a binding reaction of twoor more binding partners with high affinity and/or complementarity toensure selective hybridization under designated assay conditions.Typically, specific binding will be at least three times the standarddeviation of the background signal. Thus, under designated conditionsthe binding partner binds to its particular target molecule and does notbind in a significant amount to other molecules present in the sample.Recognition by a binder or an antibody of a particular target in thepresence of other potential interfering substances is one characteristicof such binding. Preferably, binders, antibodies or antibody fragmentsthat are specific for or bind specifically to a target bind to thetarget with higher affinity than binding to other non-target substances.Also preferably, binders, antibodies or antibody fragments that arespecific for or bind specifically to a target avoid binding to asignificant percentage of non-target substances, e.g., non-targetsubstances present in a testing sample. In some embodiments, binders,antibodies or antibody fragments of the present disclosure avoid bindinggreater than about 90% of non-target substances, although higherpercentages are clearly contemplated and preferred. For example,binders, antibodies or antibody fragments of the present disclosureavoid binding about 91%, about 92%, about 93%, about 94%, about 95%,about 96%, about 97%, about 98%, about 99%, and about 99% or more ofnon-target substances. In other embodiments, binders, antibodies orantibody fragments of the present disclosure avoid binding greater thanabout 10%, 20%, 30%, 40%, 50%, 60%, or 70%, or greater than about 75%,or greater than about 80%, or greater than about 85% of non-targetsubstances.

The term “antibody” as used herein may include an entire immunoglobulinor antibody or any functional fragment of an immunoglobulin moleculewhich is capable of specific binding to an antigen, such as acarbohydrate, polynucleotide, lipid, polypeptide, or a small molecule,etc., through at least one antigen recognition site, located in thevariable region of the immunoglobulin molecule, and can be animmunoglobulin of any class, e.g., IgG, IgM, IgA, IgD and IgE. IgY,which is the major antibody type in avian species such as chicken, isalso included. An antibody may include the entire antibody as well asany antibody fragments capable of binding the antigen or antigenicfragment of interest. Examples include complete antibody molecules,antibody fragments, such as Fab, F(ab′)2, CDRs, VL, VH, and any otherportion of an antibody which is capable of specifically binding to anantigen. Antibodies used herein are immunoreactive or immunospecificfor, and therefore specifically and selectively bind to, for example,proteins either detected (i.e., biological targets) or used fordetection (i.e., probes) in the assays of the invention. An antibody asused herein can be specific for any of the biological targets disclosedherein or any combinations thereof. In certain embodiments, a biologicaltarget itself of the present disclosure can be an antibody or fragmentsthereof.

As used herein, a “fragment thereof” “region thereof” and “portionthereof” can refer to fragments, regions and portions that substantiallyretain at least one function of the full length polypeptide.

As used herein, the term “antigen” may refer to a target molecule thatis specifically bound by an antibody through its antigen recognitionsite. The antigen may be monovalent or polyvalent, i.e., it may have oneor more epitopes recognized by one or more antibodies. Examples of kindsof antigens that can be recognized by antibodies include polypeptides,oligosaccharides, glycoproteins, polynucleotides, lipids, or smallmolecules, etc.

As used herein, the term “epitope” can refer to a peptide sequence of atleast about 3 to 5, preferably about 5 to 10 or 15, and not more thanabout 1,000 amino acids (or any integer there between), which define asequence that by itself or as part of a larger sequence, binds to anantibody generated in response to such sequence. There is no criticalupper limit to the length of the fragment, which may, for example,comprise nearly the full-length of the antigen sequence, or even afusion protein comprising two or more epitopes from the target antigen.An epitope for use in the subject invention is not limited to a peptidehaving the exact sequence of the portion of the parent protein fromwhich it is derived, but also encompasses sequences identical to thenative sequence, as well as modifications to the native sequence, suchas deletions, additions and substitutions (conservative in nature).

The terms “complementary” and “substantially complementary” may includethe hybridization or base pairing or the formation of a duplex betweennucleotides or nucleic acids, for instance, between the two strands of adouble-stranded DNA molecule or between an oligonucleotide primer and aprimer binding site on a single-stranded nucleic acid. Complementarynucleotides are, generally, A and T (or A and U), or C and G. Twosingle-stranded RNA or DNA molecules are said to be substantiallycomplementary when the nucleotides of one strand, optimally aligned andcompared and with appropriate nucleotide insertions or deletions, pairwith at least about 80% of the other strand, usually at least about 90%to about 95%, and even about 98% to about 100%. In one aspect, twocomplementary sequences of nucleotides are capable of hybridizing,preferably with less than 25%, more preferably with less than 15%, evenmore preferably with less than 5%, most preferably with no mismatchesbetween opposed nucleotides. Preferably the two molecules will hybridizeunder conditions of high stringency.

“Hybridization” as used herein may refer to the process in which twosingle-stranded polynucleotides bind non-covalently to form a stabledouble-stranded polynucleotide. In one aspect, the resultingdouble-stranded polynucleotide can be a “hybrid” or “duplex.”“Hybridization conditions” typically include salt concentrations ofapproximately less than 1 M, often less than about 500 mM and may beless than about 200 mM. A “hybridization buffer” includes a bufferedsalt solution such as 5% SSPE, or other such buffers known in the art.Hybridization temperatures can be as low as 5° C., but are typicallygreater than 22° C., and more typically greater than about 30° C., andtypically in excess of 37° C. Hybridizations are often performed understringent conditions, i.e., conditions under which a sequence willhybridize to its target sequence but will not hybridize to other,non-complementary sequences. Stringent conditions are sequence-dependentand are different in different circumstances. For example, longerfragments may require higher hybridization temperatures for specifichybridization than short fragments. As other factors may affect thestringency of hybridization, including base composition and length ofthe complementary strands, presence of organic solvents, and the extentof base mismatching, the combination of parameters is more importantthan the absolute measure of any one parameter alone. Generallystringent conditions are selected to be about 5° C. lower than the T_(m)for the specific sequence at a defined ionic strength and pH. Themelting temperature T_(m) can be the temperature at which a populationof double-stranded nucleic acid molecules becomes half dissociated intosingle strands. Several equations for calculating the T_(m) of nucleicacids are well known in the art. As indicated by standard references, asimple estimate of the T_(m) value may be calculated by the equation,T_(m)=81.5+0.41 (% G+C), when a nucleic acid is in aqueous solution at 1M NaCl (see e.g., Anderson and Young, Quantitative Filter Hybridization,in Nucleic Acid Hybridization (1985)). Other references (e.g., Allawiand SantaLucia, Jr., Biochemistry, 36:10581-94 (1997)) includealternative methods of computation which take structural andenvironmental, as well as sequence characteristics into account for thecalculation of T_(m).

In general, the stability of a hybrid is a function of the ionconcentration and temperature. Typically, a hybridization reaction isperformed under conditions of lower stringency, followed by washes ofvarying, but higher, stringency. Exemplary stringent conditions includea salt concentration of at least 0.01 M to no more than 1 M sodium ionconcentration (or other salt) at a pH of about 7.0 to about 8.3 and atemperature of at least 25° C. For example, conditions of 5×SSPE (750 mMNaCl, 50 mM sodium phosphate, 5 mM EDTA at pH 7.4) and a temperature ofapproximately 30° C. are suitable for allele-specific hybridizations,though a suitable temperature depends on the length and/or GC content ofthe region hybridized. In one aspect, “stringency of hybridization” indetermining percentage mismatch can be as follows: 1) high stringency:0.1×SSPE, 0.1% SDS, 65° C.; 2) medium stringency: 0.2×SSPE, 0.1% SDS,50° C. (also referred to as moderate stringency); and 3) low stringency:1.0×SSPE, 0.1% SDS, 50° C. It is understood that equivalent stringenciesmay be achieved using alternative buffers, salts and temperatures. Forexample, moderately stringent hybridization can refer to conditions thatpermit a nucleic acid molecule such as a probe to bind a complementarynucleic acid molecule. The hybridized nucleic acid molecules generallyhave at least 60% identity, including for example at least any of 70%,75%, 80%, 85%, 90%, or 95% identity. Moderately stringent conditions canbe conditions equivalent to hybridization in 50% formamide, 5×Denhardt'ssolution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE,0.2% SDS, at 42° C. High stringency conditions can be provided, forexample, by hybridization in 50% formamide, 5×Denhardt's solution,5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1%SDS at 65° C. Low stringency hybridization can refer to conditionsequivalent to hybridization in 10% formamide, 5×Denhardt's solution,6×SSPE, 0.2% SDS at 22° C., followed by washing in 1×SSPE, 0.2% SDS, at37° C. Denhardt's solution contains 1% Ficoll, 1% polyvinylpyrolidone,and 1% bovine serum albumin (BSA). 20×SSPE (sodium chloride, sodiumphosphate, ethylene diamide tetraacetic acid (EDTA)) contains 3M sodiumchloride, 0.2M sodium phosphate, and 0.025 M EDTA. Other suitablemoderate stringency and high stringency hybridization buffers andconditions are well known to those of skill in the art and aredescribed, for example, in Sambrook et al., Molecular Cloning: ALaboratory Manual, 2nd ed., Cold Spring Harbor Press, Plainview, N.Y.(1989); and Ausubel et al., Short Protocols in Molecular Biology, 4thed., John Wiley & Sons (1999).

Alternatively, substantial complementarity exists when an RNA or DNAstrand will hybridize under selective hybridization conditions to itscomplement. Typically, selective hybridization will occur when there isat least about 65% complementary over a stretch of at least 14 to 25nucleotides, preferably at least about 75%, more preferably at leastabout 90% complementary. See M. Kanehisa, Nucleic Acids Res. 12:203(1984).

A “primer” used herein can be an oligonucleotide, either natural orsynthetic, that is capable, upon forming a duplex with a polynucleotidetemplate, of acting as a point of initiation of nucleic acid synthesisand being extended from its 3′ end along the template so that anextended duplex is formed. The sequence of nucleotides added during theextension process is determined by the sequence of the templatepolynucleotide. Primers usually are extended by a DNA polymerase.

“Ligation” may refer to the formation of a covalent bond or linkagebetween the termini of two or more nucleic acids, e.g., oligonucleotidesand/or polynucleotides, in a template-driven reaction. The nature of thebond or linkage may vary widely and the ligation may be carried outenzymatically or chemically. As used herein, ligations are usuallycarried out enzymatically to form a phosphodiester linkage between a 5′carbon terminal nucleotide of one oligonucleotide with a 3′ carbon ofanother nucleotide.

“Sequencing,” “sequence determination” and the like means determinationof information relating to the nucleotide base sequence of a nucleicacid. Such information may include the identification or determinationof partial as well as full sequence information of the nucleic acid.Sequence information may be determined with varying degrees ofstatistical reliability or confidence. In one aspect, the term includesthe determination of the identity and ordering of a plurality ofcontiguous nucleotides in a nucleic acid. “High throughput digitalsequencing” or “next generation sequencing” means sequence determinationusing methods that determine many (typically thousands to billions) ofnucleic acid sequences in an intrinsically parallel manner, i.e. whereDNA templates are prepared for sequencing not one at a time, but in abulk process, and where many sequences are read out preferably inparallel, or alternatively using an ultra-high throughput serial processthat itself may be parallelized. Such methods include but are notlimited to pyrosequencing (for example, as commercialized by 454 LifeSciences, Inc., Branford, Conn.); sequencing by ligation (for example,as commercialized in the SOLiD™ technology, Life Technologies, Inc.,Carlsbad, Calif.); sequencing by synthesis using modified nucleotides(such as commercialized in TruSeq™ and HiSeg™ technology by Illumina,Inc., San Diego, Calif.; HeliScope™ by Helicos Biosciences Corporation,Cambridge, Mass.; and PacBio RS by Pacific Biosciences of California,Inc., Menlo Park, Calif.), sequencing by ion detection technologies(such as Ion Torrent™ technology, Life Technologies, Carlsbad, Calif.);sequencing of DNA nanoballs (Complete Genomics, Inc., Mountain View,Calif.); nanopore-based sequencing technologies (for example, asdeveloped by Oxford Nanopore Technologies, LTD, Oxford, UK), and likehighly parallelized sequencing methods.

“SNP” or “single nucleotide polymorphism” may include a geneticvariation between individuals; e.g., a single nitrogenous base positionin the DNA of organisms that is variable. SNPs are found across thegenome; much of the genetic variation between individuals is due tovariation at SNP loci, and often this genetic variation results inphenotypic variation between individuals. SNPs for use in the presentinvention and their respective alleles may be derived from any number ofsources, such as public databases (U.C. Santa Cruz Human Genome BrowserGateway (genome.ucsc.edu/cgi-bin/hgGateway) or the NCBI db SNP website(www.ncbi.nlm.nih gov/SNP/), or may be experimentally determined asdescribed in U.S. Pat. No. 6,969,589; and US Pub. No. 2006/0188875entitled “Human Genomic Polymorphisms.” Although the use of SNPs isdescribed in some of the embodiments presented herein, it will beunderstood that other biallelic or multi-allelic genetic markers mayalso be used. A biallelic genetic marker is one that has two polymorphicforms, or alleles. As mentioned above, for a biallelic genetic markerthat is associated with a trait, the allele that is more abundant in thegenetic composition of a case group as compared to a control group istermed the “associated allele,” and the other allele may be referred toas the “unassociated allele.” Thus, for each biallelic polymorphism thatis associated with a given trait (e.g., a disease or drug response),there is a corresponding associated allele. Other biallelicpolymorphisms that may be used with the methods presented hereininclude, but are not limited to multinucleotide changes, insertions,deletions, and translocations. It will be further appreciated thatreferences to DNA herein may include genomic DNA, mitochondrial DNA,episomal DNA, and/or derivatives of DNA such as amplicons, RNAtranscripts, cDNA, DNA analogs, etc. The polymorphic loci that arescreened in an association study may be in a diploid or a haploid stateand, ideally, would be from sites across the genome.

As used herein, the term “microfluidic device” may generally refer to adevice through which materials, particularly fluid borne materials, suchas liquids, can be transported, in some embodiments on a micro-scale,and in some embodiments on a nanoscale. Thus, the microfluidic devicesdescribed by the presently disclosed subject matter can comprisemicroscale features, nanoscale features, and combinations thereof.

Accordingly, an exemplary microfluidic device typically comprisesstructural or functional features dimensioned on the order of amillimeter-scale or less, which are capable of manipulating a fluid at aflow rate on the order of a μL/min or less. Typically, such featuresinclude, but are not limited to channels, fluid reservoirs, reactionchambers, mixing chambers, and separation regions. In some examples, thechannels include at least one cross-sectional dimension that is in arange of from about 0.1 μm to about 500 μm. The use of dimensions onthis order allows the incorporation of a greater number of channels in asmaller area, and utilizes smaller volumes of fluids.

A microfluidic device can exist alone or can be a part of a microfluidicsystem which, for example and without limitation, can include: pumps forintroducing fluids, e.g., samples, reagents, buffers and the like, intothe system and/or through the system; detection equipment or systems;data storage systems; and control systems for controlling fluidtransport and/or direction within the device, monitoring and controllingenvironmental conditions to which fluids in the device are subjected,e.g., temperature, current, and the like.

As used herein, the terms “channel,” “micro-channel,” “fluidic channel,”and “microfluidic channel” are used interchangeably and can mean arecess or cavity formed in a material by imparting a pattern from apatterned substrate into a material or by any suitable material removingtechnique, or can mean a recess or cavity in combination with anysuitable fluid-conducting structure mounted in the recess or cavity,such as a tube, capillary, or the like. In the present invention,channel size means the cross-sectional area of the microfluidic channel.

As used herein, the terms “flow channel” and “control channel” are usedinterchangeably and can mean a channel in a microfluidic device in whicha material, such as a fluid, e.g., a gas or a liquid, can flow through.More particularly, the term “flow channel” refers to a channel in whicha material of interest, e.g., a solvent or a chemical reagent, can flowthrough. Further, the term “control channel” refers to a flow channel inwhich a material, such as a fluid, e.g., a gas or a liquid, can flowthrough in such a way to actuate a valve or pump.

As used herein, “chip” may refer to a solid substrate with a pluralityof one-, two- or three-dimensional micro structures or micro-scalestructures on which certain processes, such as physical, chemical,biological, biophysical or biochemical processes, etc., can be carriedout. The micro structures or micro-scale structures such as, channelsand wells, electrode elements, electromagnetic elements, areincorporated into, fabricated on or otherwise attached to the substratefor facilitating physical, biophysical, biological, biochemical,chemical reactions or processes on the chip. The chip may be thin in onedimension and may have various shapes in other dimensions, for example,a rectangle, a circle, an ellipse, or other irregular shapes. The sizeof the major surface of chips of the present invention can varyconsiderably, e.g., from about 1 mm² to about 0.25 m². Preferably, thesize of the chips is from about 4 mm² to about 25 cm² with acharacteristic dimension from about 1 mm to about 5 cm. The chipsurfaces may be flat, or not flat. The chips with non-flat surfaces mayinclude channels or wells fabricated on the surfaces.

A microfluidic chip can be used for the methods and assay systemsdisclosed herein. A microfluidic chip can be made from any suitablematerials, such as PDMS (Polydimethylsiloxane), glass, PMMA(polymethylmethacrylate), PET (polyethylene terephthalate), PC(Polycarbonate), etc., or a combination thereof.

“Multiplexing” or “multiplex assay” herein may refer to an assay orother analytical method in which the presence and/or amount of multipletargets, e.g., multiple nucleic acid target sequences, can be assayedsimultaneously by using more than one capture probe conjugate, each ofwhich has at least one different detection characteristic, e.g.,fluorescence characteristic (for example excitation wavelength, emissionwavelength, emission intensity, FWHM (full width at half maximum peakheight), or fluorescence lifetime) or a unique nucleic acid or proteinsequence characteristic.

Assays for Determining Spatial Patterns of Biological Targets

Disclosed herein are spatially-encoded, multiplexed methods and assaysystems capable of high levels of multiplexing with an efficient spatialencoding scheme. In one embodiment, provided herein is instrumentationcapable of delivering reagents to a sample and thereby spatiallyencoding multiple sites to which the reagents are delivered. In oneaspect, reagents can be delivered to a sample according to a knownspatial pattern, for example, a spatial pattern determined byhistological features of the sample. In another aspect, reagents aredelivered by random-access methods, such as inkjet and pin-spotting. Inanother aspect, microfluidic devices with addressing channels and thelike are used to deliver reagents to a sample, and to spatially encodemultiple sites in the sample to which the reagents are delivered. Insome embodiments, the spatially-encoded (“addressed,” or “addresstagged”), multiplexed methods and assay systems comprise a decodingfeature determined by a readout that is digital in nature. In oneaspect, the methods and assay systems disclosed herein detect thepresence or absence of a biological target or a biological activityindicative of a biological target. In another aspect, provided hereinare methods and assay systems that can detect the amount or abundance ofa biological target or biological activity indicative of a biologicaltarget at multiple sites in a sample, as well as the location of each ofthe multiple sites in the sample. Based on the analysis of the amount orabundance and the location information of one or more biological targetsor activities, spatial patterns across the multiple sites in the samplecan be generated. In any of the preceding embodiments, the method orassay system may not depend on an imaging technique for determiningspatial or location information of the one or more biological targets inthe sample, although the method or assay system may optionally compriseusing an imaging technique for other purposes. Imaging techniques mayinclude but are not limited to conventional immunohistochemical (IHC)imaging and immunofluorescence (IF) imaging. Methods and assays systemsto determine a spatial pattern of abundance and/or activity of abiological target in a sample are disclosed in detail in U.S.application Ser. No. 13/080,616, entitled “Spatially encoded biologicalassays” (Pub. No. US 2011/0245111), the disclosure of which isincorporated herein by reference for all purposes.

The present disclosure further provides instrumentation with an abilityto deliver reagents to multiple sites in a sample, wherein each of themultiple sites can be identified by the reagents delivered thereto. Inone embodiment, reagents are delivered in a spatially-defined pattern.The instrumentation, together with software, reagents and protocols,provides a key component of the methods and assay systems of the presentdisclosure, allowing for measurement of numerous biological targets oractivities, including DNA, RNA and/or protein expression, and spatiallocalization of such biological targets or activities in a sample. Inone embodiment, the abundance, expression, and/or activity and thelocation of biological targets in the biological samples are determinedafter the assay products of the multiplexed assay are removed from thebiological sample and pooled for analysis. Determination of theabundance, expression, and/or activity and the location of biologicaltargets can be performed by, e.g., next-generation sequencing, whicheasily provides millions to trillions of data points at low cost. Theassay results such as the amount or activity of biological targets canthen be mapped back to a specific location in the biological sample. Themethods and assay systems provide tools to analyze the complex spatialpatterns of cellular function and regulation in biological samples.

In one aspect, a method of determining a spatial pattern of abundance,expression, and/or activity of one or more biological targets acrossmultiple sites in a sample is provided in FIG. 1. At Step 110, a probefor each of one or more biological targets is delivered to multiplesites in a sample, each probe comprising a target-binding moiety, anaddress tag that identifies each site to which the probe is delivered,and an identity tag.

In any of the embodiments of the present disclosure, the sample can beany biological sample or samples that can be affixed to a support orprovided essentially in a two-dimensional manner, such that an assayedbiological target or activity can be tied back to the location withinthe biological sample. In certain embodiments, the sample can be afreshly isolated sample, a fixed sample, a frozen sample, an embeddedsample, a processed sample, or a combination thereof. Exemplary samplesof the present disclosure include tissue sections (e.g., including wholeanimal sectioning and tissue biopsies), cell populations, or otherbiological structure disposed upon a support, such as on a slide (e.g.,a microscope slide) or culture dish, and the like. In preferredembodiments, the methods and assay systems of the present disclosure arecompatible with numerous biological sample types, including freshsamples, such as primary tissue sections, and preserved samplesincluding but not limited to frozen samples and formalin-fixed,paraffin-embedded (FFPE) samples. In certain embodiments, the sample canbe fixed with a suitable concentration of formaldehyde orparaformaldehyde, for example, 4% of formaldehyde or paraformaldehyde inphosphate buffered saline (PBS). In certain embodiments, the biologicalsamples are immobilized on a substrate surface having discrete,independently measureable areas.

In one embodiment, the biological sample may contain one or morebiological targets of interest. In any of the embodiment of the presentdisclosure, the one or more biological targets can be any biologicalmolecules including but not limited to proteins, nucleic acids, lipids,carbohydrates, ions, or multicomponent complexes containing any of theabove. Examples of subcellular targets include organelles, e.g.,mitochondria, Golgi apparatus, endoplasmic reticulum, chloroplasts,endocytic vesicles, exocytic vesicles, vacuoles, lysosomes, etc. In someembodiments, the one or more biological targets can be nucleic acids,including RNA transcripts, genomic DNA sequences, cDNAs, amplicons, orother nucleic acid sequences. In other embodiments, the one or morebiological targets can be proteins, enzymes (protein enzymes orribozymes) and the like.

At Step 110, the probe for each of the multiple biological targetscomprise: (1) a target-binding moiety capable of binding to the probe'scorresponding biological target; (2) an address tag that identifies eachsite to which the probe is delivered; and (3) an identity tag thatidentifies the probe's corresponding biological target or target-bindingmoiety. Depending on the nature of the biological target, thetarget-binding moiety can be a target-specific nucleotide sequence (forexample, a sequence complementary to a sequence of a nucleic acidtarget), small molecule, aptamer, antibody, lipid, carbohydrate, ion,affinity capture agent, or multicomponent complexes containing any ofthe above. The address tag identifies the position in the sample towhich the probe is delivered, and the identity tag identifies theprobe's corresponding biological target being assayed or thetarget-binding moiety. Thus, the identities of the address tag and theidentity tag can be used to link assay results to biological targets andlocations in the sample. In preferred embodiments, there can be at leasttwo address tags for a biological target at each of multiple sites in asample, each address tag identifying a parameter of each of the multiplesites. For example, there can be an X-axis address tag and a Y-axisaddress tag for each site in a sample placed on an X-Y coordinate plane.Thus, each site can be uniquely identified by its corresponding (X, Y)coordinates. In preferred embodiments of the present disclosure, theaddress tags and/or the identity tags can be oligonucleotides. In otherembodiments, the address tags and/or the identity tags can be mass tags,fluorescent labels, or other moieties.

In some embodiments, the target-binding moiety, address tag, and/oridentity tag of the probe are pre-coupled before being delivered to thebiological sample. In the case where the probes are oligonucleotides,the target-binding sequence, address tag sequence, and/or identity tagsequence can be synthesized as a single oligonucleotide. Alternatively,the target-binding moiety, address tag, and/or identity tag of the probecan be synthesized or obtained separately and combined before deliveryto the biological sample. For example, two separate oligonucleotides canbe synthesized and coupled by, e.g., ligation; or an antibody and anoligonucleotide can be prepared separately and conjugated beforedelivery to the biological sample. In other embodiments, the probes andthe address tags can be synthesized separately, and delivered to thebiological sample at different steps (e.g., probes first and addresstags thereafter, or vice versa) in the assay.

At Step 120, the probe is allowed to bind to its correspondingbiological target in the sample and thereby to react or interact withthe biological target. For example, conditions are provided to allowoligonucleotides to hybridize to nucleic acid targets, enzymes tocatalyze reactions with protein targets, antibodies to bind epitopeswithin a target, etc. In the case where the biological targets arenucleic acids, the probes are typically oligonucleotides and hybridizeto the target nucleic acids. In the case that the biological targets areproteins, the probes typically are aptamers, small molecules, oroligonucleotide-conjugated proteins that interact with target proteinsby binding to them or by reacting with them (that is, one of theproteins is a substrate for the other). Oligonucleotides may be coupledto the probes or proteins by conjugation, chemical or photo-crosslinkingvia suitable groups and the like.

In some embodiments, after allowing the probes to bind to or interactwith the one or more biological targets in the sample, probes bound tothe biological targets may be separated from probes delivered to thesample but not bound to the biological targets. In one aspect, in thecase where the biological targets are nucleic acids and the probes areoligonucleotides, the separation can be accomplished by, e.g., washingthe unhybridized probes from the sample. Similarly, for other assaysthat are based on affinity binding, including those using aptamer, smallmolecule, and protein probes, washing steps can be used to remove lowaffinity binders. In the case where the probe is transformed viainteraction with the target, e.g., in the case of a peptide, e.g., viacleavage by a protease or phosphorylation by a kinase, it is convenientto collect all probes, including both probes that have interacted withthe biological targets and thus transformed and probes not transformed.After collection or pooling, an antibody or other affinity capture agentcan be used to capture probes transformed by addition of a moiety (e.g.,a phosphate group in cases of phosphorylation by a kinase). In caseswhere probes have been transformed via cleavage, the transformed probescan be separated, e.g., by capturing the non-transformed probes via atag that is removed from the transformed probes during thetransformation (e.g., by cleavage), or by adding a new tag at the siteof cleavage.

In certain other embodiments, probes bound to the biological targets maynot need to be separated from probes not bound to the biological targetsfor determining a spatial pattern of abundance, expression, and/oractivity of the biological targets. At Step 130, probes bound to the oneor more biological targets are analyzed. In certain embodiments, theanalysis comprises determining abundance, expression, and/or activity ofeach biological target and the identities of the identity tag and theaddress tag for each biological target at each site. Numerous methodscan be used to identify the address tags, identity tags and/ortarget-binding moieties of the probes of the methods and assay systemsdisclosed herein. The address tags can be detected using techniques suchas mass spectroscopy (e.g., matrix-assisted laserdesorption/ionization-time of flight mass spectrometry (MALDI-TOF),LC-MS/MS, and TOF/TOF™ LC/MS/MS), nuclear magnetic resonance imaging,or, preferably, nucleic acid sequencing. Examples of techniques fordecoding the probes of the present invention can be found, for example,in US Pub. No. 20080220434, which is incorporated herein by reference.For example, the address tags may be oligonucleotide mass tags (OMTs ormassTags). Such tags are described, e.g., in US Pub. No. 20090305237,which is incorporated by reference in its entirety. In yet anotheraspect, the probes can be amplified and hybridized to a microarray. Thiswould require separate amplification reactions to be carried out, inwhich each amplification is specific to a particular address tag orsubset of tags, accomplished by using tag-specific primers. Eachamplification would also incorporate a different resolvable label (e.g.fluorophor). Following hybridization, the relative amounts of aparticular target mapping to different spatial locations in the samplecan be determined by the relative abundances of the resolvable labels.At Step 140, based on the analysis of probes bound to the one or morebiological targets, a spatial pattern of abundance, expression, and/oractivity of the one or more biological targets across the multiple sitesin the sample is determined.

In a preferred aspect, the probes according to the present disclosureare substrates for high-throughput, next-generation sequencing, andhighly parallel next-generation sequencing methods are used to confirmthe sequence of the probes (including, for example, the sequence of thetarget-binding moiety, the address tag, and/or the identity tag).Suitable sequencing technologies include but are not limited to SOLiD™technology (Life Technologies, Inc.) or Genome Ananlyzer (Illumina,Inc.). Such next-generation sequencing methods can be carried out, forexample, using a one pass sequencing method or using paired-endsequencing. Next generation sequencing methods include, but are notlimited to, hybridization-based methods, such as disclosed in e.g.,Drmanac, U.S. Pat. Nos. 6,864,052; 6,309,824; and 6,401,267; and Drmanacet al., U.S. patent publication 2005/0191656; sequencing-by-synthesismethods, e.g., U.S. Pat. Nos. 6,210,891; 6,828,100; 6,969,488;6,897,023; 6,833,246; 6,911,345; 6,787,308; 7,297,518; 7,462,449 and7,501,245; US Publication Application Nos. 20110059436; 20040106110;20030064398; and 20030022207; Ronaghi, et al., Science, 281:363-365(1998); and Li, et al., Proc. Natl. Acad. Sci., 100:414-419 (2003);ligation-based methods, e.g., U.S. Pat. Nos. 5,912,148 and 6,130,073;and U.S. Pat. Appln Nos. 20100105052, 20070207482 and 20090018024;nanopore sequencing, e.g., U.S. Pat. Appln Nos. 20070036511;20080032301; 20080128627; 20090082212; and Soni and Meller, Clin Chem53:1996-2001 (2007), as well as other methods, e.g., U.S. Pat. ApplnNos. 20110033854; 20090264299; 20090155781; and 20090005252; also, see,McKernan, et al., Genome Res. 19:1527-41 (2009) and Bentley, et al.,Nature 456:53-59 (2008), all of which are incorporated herein in theirentirety for all purposes.

In preferred embodiments, probes bound to the one or more biologicaltargets are analyzed by sequencing. Such analysis by sequencingcomprises determining the amount of a sequencing product, whichindicates abundance, expression, and/or activity of each biologicaltarget, the sequencing product comprising all or a portion of theaddress tag sequence and all or a portion of the identity tag sequenceidentifying each biological target at each site. In one embodiment, theaddress tag sequence of the sequencing product allows the mapping of theassay results back to the multiple sites in the sample.

In certain embodiments, two probes that bind to the same target molecule(for example, two polynucleotide probes that hybridize to adjacent siteson a nucleic acid target) may be assayed by extension followed byligation (the extension-ligation assay). The extension-ligation assayallows certain target sequence to be determined de novo. For example, ifthe primer and the downstream oligo are separated by 20 bases andreverse transcriptase is used to fill this 20-base gap, 20 bases ofsequence of the RNA target can be obtained. In certain embodiments, byusing the extension-ligation assay in the present methods or assaysystems, regions of sequence that are of particular interest may becharacterized. For example, these regions may comprise mutations orvariations, for example, with implications in cancer, MHC variations,and RNA editing.

In any of the embodiments disclosed herein, an extension assay may alsobe used and may allow certain target sequences, for example, nucleotidesequences, to be determined de novo. In one embodiment, an extensionassay of the present disclosure may be performed as follows. A firstprimer may be used to make cDNA from a target sequence. In certainembodiments, the first primer can be a random primer (e.g., randomhexamer) or a sequence-specific primer. A random primer can be used tomake cDNA from the entire transcriptome, while a sequence-specificprimer may be used to make cDNA from a specific target sequence. Incertain aspects, the first primer may comprise a universal priming sitefor amplification of the assay products, an adaptor to enable sequenceidentification by sequencing techniques, and/or an adaptor for attachingaddress tags. In other embodiments, the first primer may be conjugatedto an adaptor for attaching address tags. The X and Y address tags asdescribed infra can be coupled to the first primer via the adaptor. Notethat the X and Y address tags can be coupled to the same or differentside relative to the target sequence, and the configuration may be usedin any of embodiments disclosed herein. The Y address tag can be furtherlinked to a universal priming site or an adaptor for sequencing coupledto biotin. The cDNA with conjugated X and Y address tags are then elutedand captured on a streptavidin bead, and a second primer can then beinstalled to the cDNA on the opposite side relative to the first primer.In some embodiments, capture of the polynucleotide sequence can be basedon other hapten-binder combinations other than biotin-streptavidin, orbe sequence-based. In certain embodiments, the second primer can be arandom primer (e.g., random hexamer) or a sequence-specific primer. Incertain aspects, the second primer may comprise a universal priming sitefor amplification of the assay products, an adaptor to enable sequenceidentification by sequencing techniques, and/or an adaptor for attachingaddress tags. In other embodiments, the second primer may be conjugatedto a universal priming site or an adaptor for sequencing. Together withthe priming site or adaptor coupled to biotin, the sequence can beextended from the second primer, amplified, and sequenced.

The methods and assay systems disclosed herein may comprise anamplification step, and in particular, a nucleic acid amplificationstep. In certain aspects, the amplification step is performed by PCR. Insome embodiments, linear amplification (e.g., by T7 RNA polymerase) maybe used instead of PCR or as a partial replacement for PCR. In oneaspect, linear amplification of polynucleotides may cause lessdistortion of the relative abundances of different sequences. This canbe accomplished by including a T7 RNA pol promoter in one of theuniversal portions of the sequence. In this case, the promoter itselfand regions upstream of the promoter are not copied. In yet otherembodiments, other amplification methods may be used in the methods andassay systems disclosed herein. For some sequencing methods (e.g.,nanopore sequencing), amplification may be optional.

The T7 RNA polymerase based amplification is a commonly used protocolfor mRNA amplification originally described by van Gelder et al., Proc.Natl. Acad. Sci. USA 87, 1663-1667 (1990). The protocol consists of thesynthesis of a cDNA complementary to the mRNA (“first strandsynthesis”), effected by reverse transcription, followed by secondstrand synthesis to yield double-stranded cDNA, and in vitrotranscription using the double-stranded cDNA as template effected withT7 RNA polymerase. The last step provides single-stranded antisense RNA(aRNA), which may be labeled in case labeled nucleotides are provided.The nucleotides may be labeled by radioactive labeling ornon-radioactive labeling methods. Eberwine et al. (Proc. Natl. Acad.Sci. USA 89, 3010-3014 (1992)) extended van Gelder's method by adding asecond round of amplification using the RNA obtained in the first roundas template. Wang et al. (Nature Biotechnol. 18, 457-459 (2000))provided a variant of the original T7 method, characterized by amodified second strand synthesis method. The second strand synthesismethod of Wang et al. is known in the art as the SMART™ technology(Clontech) for cDNA synthesis. Baugh et al. (Nucleic Acids Res. 29, E29(2001)) describe an optimized variant of the method according to vanGelder et al. and analyze the performance on Affymetrix DNA chips(GeneChip®). Affymetrix GeneChips are designed to probe the anti-sensestrand. Any other DNA chip or microarray probing the anti-sense strandmay be envisaged when performing a T7 RNA amplification, whereinlabeling occurs during the in vitro transcription step.

In other embodiments, amplification techniques such as rolling circleamplification (RCA) and circle to circle amplification (C2CA) may beused for probe, target, tag, and/or signal amplification of the presentdisclosure. RCA is a linear-isothermal process in the presence ofcertain DNA polymerases, using an ssDNA mini-circle as a template (Fireand Xu, Proc. Natl. Acad. Sci., 92: 4641-4645 (1995); Daubendiek et al.,J. Am. Chem. Soc. 117:77818-7819 (1995)). In certain aspects, apolynucleotide sequence can be replicated about 500 to 1000 times,depending on the amplification time. For example, in a dual targetingassay for a target protein as discussed supra, a linear ligated productis formed (e.g., when two antibodies bind to adjacent domains on atarget protein, the antibodies' oligonucleotide tags can be ligated),and can be cut by restriction enzymes and then re-ligated to form a DNAcircle by a DNA ligase and a template. In certain embodiments, phi29 DNApolymerase can be used to extend the primer, which is also the template,to form a long ssDNA containing a number of sequences complementary tothe initial DNA circle. C2CA is based on RCA, and may include threesteps: replication, monomerization and ligation (Dahl et al., Proc.Natl. Acad. Sci., 101: 4548-4553 (2004)). The original circular DNA isconsidered as the positive polarity. After one step of replication (RCAreaction), the product is converted into the opposite polarity.Restriction oligos with the positive polarity (RO⁺) can form duplexregions with the RCA product, and the duplex regions can be cleaved byrestriction enzymes to generate monomers. Then the monomers can beguided into a ligation step and circularized. These circles serve as thetemplates for the next round of RCA, primed by the RO⁺. The process canbe further repeated to produce around 100-fold higher concentration oftarget sequences than conventional PCR.

In another aspect, as shown in FIG. 2, a method of determining a spatialpattern of abundance, expression, and/or activity of one or morebiological targets across multiple sites in a sample is provided,featuring an efficient implementation of an address tagging scheme forthe one or more biological targets across the multiple sites. In oneembodiment, the address tagging scheme is a combinatorial scheme usingat least two address tags for the biological targets for each of themultiple sites in the sample. At Step 210, a probe for each of one ormore biological targets to multiple sites in a sample is delivered, eachprobe comprising (1) a target-binding moiety capable of binding to theprobe's corresponding biological target; and (2) an identity tag thatidentifies the probe's corresponding biological target or target-bindingmoiety. Depending on the nature of the biological target, thetarget-binding moiety can be a target-specific nucleotide sequence (forexample, a sequence complementary to a sequence of a nucleic acidtarget), small molecule, aptamer, antibody, lipid, carbohydrate, ion,affinity capture agent, or multicomponent complexes containing any ofthe above. At Step 220, each probe is allowed to interact with or bindto its corresponding biological target in the sample, under appropriateconditions.

In certain embodiments, probes not bound to the biological targets maybe removed, and thereby separated from probes bound to the biologicaltargets. Such separation can be performed essentially as discussedabove, for example, by washing the sample to remove unhybridizedoligonucleotide probes. In certain other embodiments, probes bound tothe biological targets may not need to be separated from probes notbound to the biological targets for determining a spatial pattern ofabundance, expression, and/or activity of the biological targets.

Next, at Step 230, an address tag is delivered to each of the multiplesites in the sample, and the address tag is to be coupled to the probefor each biological target and identifies each site to which the addresstag is delivered. Note that in this aspect, the probe and address tagare delivered in separate steps. In certain embodiments where the probesare oligonucleotides, the address tags may be coupled to theoligonucleotide probes by various means known to the skilled artisan,for example, by extension, ligation, ligation followed by extension, orany combination thereof. For instance, the information in the addresstags can be transferred by using a DNA polymerase to extend a probeoligonucleotide that acts as a primer, and thereby copy and incorporatethe sequence of the address tags.

At Step 240, probe/address tag conjugates bound to the one or morebiological targets are analyzed. In certain embodiments, the analysiscomprises determining abundance, expression, and/or activity of eachbiological target and the identities of the identity tag and the addresstag for each biological target at each site. In one aspect, theabundance, expression, and/or activity of each biological target can beassessed by determining the amount of the probe or the probe/address tagconjugate bound to the target. Numerous methods can be used to identifythe address tags, identity tags and/or target-binding moieties of theprobes, as discussed above. In preferred embodiments, probes orprobe/address tag conjugates bound to the one or more biological targetsare analyzed by sequencing. Any suitable sequence techniques and methodsas discussed above can be used, including high-throughput,next-generation sequencing, and highly parallel next-generationsequencing methods. Preferably, in any of embodiments of the presentdisclosure, all or a portion of the address tag sequence and all or aportion of the identity tag sequence are determined from the samesequencing product. Preferably, also determined at the same time is theabundance of the sequencing product, for example, the “copy number” or“hits” of the sequencing product. The abundance of the sequencingproduct may correlate with the amount of the probe or probe/address tagconjugate bound to the target, which in turn can correlate with theabundance, expression, and/or activity of each biological target. Insome embodiments, the abundance of sequence products reveals therelative quantity of biological targets at the location.

Based on the analysis of probe/address tag conjugates bound to the oneor more biological targets at Step 240, a spatial pattern of abundance,expression, and/or activity of the one or more biological targets acrossthe multiple sites in the sample is determined at Step 250, for example,by mapping the assayed abundance, expression, and/or activity of eachbiological target back to each site of the sample.

Although individual steps are discussed in a particular order in certainembodiments to better explain the claimed subject matter, the preciseorder of the steps can be varied. For example, Steps 210 and 230 can becombined, so that a mixture of the probes and address tags is delivered.Coupling of the address tag to the probe may be carried out immediatelyafter the combined steps 210 and 230, or concomitantly with them. It cantherefore be appreciated that the address tagging of probe molecules andthe separation of probes based on their ability to interact with theircorresponding targets can be accomplished with flexibility. Similarly,there is considerable flexibility in the address tagging scheme. Asdescribed infra, the methods and assay systems disclosed herein areparticularly amenable to combinatorial methods.

Spatially Encoded Genomic Assay

In particular embodiments, the methods and assay systems can be used fornucleic acid analysis, for example, for genomic analysis, genotyping,detecting single nucleotide polymorphisms (SNPs), quantitation of DNAcopy number or RNA transcripts, localization of particular transcriptswithin samples, and the like. FIG. 3 illustrates an exemplary assay andaddress tagging scheme. For illustrative purposes, the target is anucleic acid sequence, and two oligonucleotide probes are provided, andit should be understood that the disclosed methods and assay systems canbe used for any suitable target employing one or more suitable probes.Each oligonucleotide probe comprises a target-specific region seen at305 and 307, respectively. In certain embodiments, for example fordetecting SNPs, the two target-specific regions are located on eitherside of the SNP to be analyzed. Each oligonucleotide probe alsocomprises a ligation region, seen at 301 and 303, respectively. Theoligonucleotide probes are allowed to hybridize to a target nucleic acid(not shown) in the biological sample. At Step 302, one or both of theoligonucleotide probes may be extended and ligated to the other probe toform an extended probe comprising target nucleic acid region 309 andligation regions 301 and 303. In some embodiments, the two probes areimmediately adjacent to each other, and only ligation is needed to forman extended probe. In some embodiments, Step 302 may be used toincorporate an SNP sequence or other target sequences to be assayed.

Two address tags, both comprising an address tag region (seen at 315 and317), a ligation region (seen at 311 and 313), and a primer region (seenat 319 and 321) are combined with and ligated to the extended probe atstep 304 to form a target-specific oligonucleotide. In contrast withFIG. 1, the probes and address tags are delivered at separate steps. Insome embodiments, a pair of address tags ligate specifically to one sideof the target sequence or the other (i.e., 5′ or 3′ of the targetsequence), respectively. In certain embodiments, the ligation and primerregions of the address tags and probes are universal; that is, the setof ligation and primer regions used in constructing the probes andaddress tags are constant, and only the target-specific regions of theprobes and the address tag region of the address tag differ. Inalternative embodiments, the ligation and primer regions are notuniversal and each probe and/or address tag may comprise a differentligation and/or primer region.

Following ligation, the probe/address tag conjugates are eluted, pooled,and, optionally, sequencing adaptors are added to the probe/address tagconjugates via PCR. In alternative embodiments, sequencing primers maybe ligated to the address tags, or sequencing primer sequences can beincluded as part of the address tags. As seen in FIG. 3, each sequencingadaptor comprises primer region 319 or 321, compatible with the primerregions 319 and 321 on the address tags. The final construct comprisingfirst adaptor 327, first primer region 319, first coding tag 315,ligation regions 311 and 301, target region 309, ligation regions 313and 303, second coding tag 317, second primer region 325 and secondadaptor 329 can be subject to sequencing, for example, by input into adigital high-throughput sequencing process.

A combination of extension and ligation reactions are exemplified inFIG. 3, but it should be appreciated that a variety of reactions may beused to couple the address tags to the target-specific probes, includingligation only (e.g., for oligonucleotides that hybridize to contiguousportions of the target nucleic acid sequence). Alternatively, an assayutilizing an additional oligonucleotide, such as in the GOLDENGATE®assay (Illumina, Inc., San Diego, Calif.) (see Fan, et al., Cold SpringSymp. Quant. Biol., 68:69-78 (2003)), may be employed.

To maximize the efficiency of address tagging, a combinatorial approachusing pairs of address tags can be used. By de-coupling thetarget-specific information and the spatial information in the addresstags, the number of oligonucleotides required for determining a spatialpattern of one or more biological targets across multiple sites in asample is dramatically reduced, with a concomitant decrease in cost.

FIG. 4 illustrates one embodiment of a combinatorial address taggingscheme, where nucleic acids in a representative tissue section (shown at416) are assayed. FIG. 4A shows two probe/address tag conjugates 420 and422 specifically bound to a biological target 402 of interest. The firstprobe/address tag conjugate 420 comprises address tag 408, associatedwith tag 404. Tag 404 can be a universal priming site for amplificationof the assay products or an adaptor to enable identification of theaddress tag 408 and/or other regions of probe/address tag conjugates420, for example, using sequencing technologies. The secondprobe/address tag conjugate 422 comprises address tag 406, associatedwith tag 410. Tag 410 can be a universal priming site for amplificationof the assay products or an adaptor to enable identification of theaddress tag 406 and/or other regions of probe/address tag conjugates422, for example, using sequencing technologies.

In other embodiments, a biological target 424 is assayed according tothe combinatorial address tagging scheme shown in FIG. 4D. Two probes426 and 428 specifically bind to the biological target 424 of interest.In some embodiments, a portion of each of probes 426 and 428specifically binds to the target, while each probe also has a portionthat specifically binds to an adaptor 438, for example, by specificnucleic acid hybridization. In one embodiment, the probe or probesspecifically hybridize to the adaptor. In cases where the biologicaltarget is a nucleic acid and the probes are oligonucleotides, theadaptor can specifically bind to the following combinations: 1) the 5′portion of probe 426 and the 3′ portion of probe 428; 2) the 3′ portionof probe 426 and the 5′ portion of probe 428; 3) the 5′ portion of probe426 and the 5′ portion of probe 428; or 4) the 3′ portion of probe 426and the 3′ portion of probe 428. In certain embodiments, probe 426 or428 is a linear molecule, a branched molecule, a circular molecule, or acombination thereof. After binding of the two probes to the biologicaltarget and the adaptor to the two probes, address tags can be deliveredto the sample and coupled to the adaptor. For example, the adaptor canbe tagged with address tag 430, associated with tag 434, and/or withaddress tag 432, associated with tag 436. Tags 434 and 436 can beuniversal priming sites for amplification of the assay products orsequences to enable identification of the address tags and/or otherregions of adaptor/address tag conjugates, for example, using sequencingtechnologies. In certain embodiments, the address tags are tagged at thesame end of the adaptor, or at different ends of the adaptor. In otherembodiments, an address tag and/or tag 434 or 436 can be pre-coupled tothe adaptor, and the adaptor/address tag or adaptor/tag conjugate orcomplex is then delivered to the sample in order to bind to the probebound to the biological target. In certain aspects, the adaptor is alinear molecule, a branched molecule, a circular molecule, or acombination thereof. In some embodiments, after an address tag isattached to each end of the adaptor, the ends can be joined. Forexample, in FIG. 4D, address tags 434 and/or 436 can comprise structuresand/or sequences that allow the two ends of the tagged adaptor 438 to bejoined to form a circular construct, to facilitate amplification and/orsequencing of the construct.

In certain embodiments, all or a portion of the adaptor/address tagconjugate sequence is determined, for example, by nucleic acidsequencing. In other embodiments, all or a portion of the probesequence, and/or all or a portion of the adaptor/address tag conjugatesequence, is determined. For example, a first address tag can be coupledto probe 426, and a second address tag can be coupled to adaptor 438.The duplex formed between probe 426 and adaptor 438 can be subjected toextension and sequencing, to generate a conjugate that comprisessequences of the first address tag, all or a portion of probe 426, allor a portion of adaptor 438, and the second address tag.

The tagging scheme is not limited to the use of two or more probes forthe same biological target. For example, in cases where one probe isused, a tag (e.g., an address tag, an adaptor for ligation, or auniversal sequencing primer or amplification primer sequence) can becoupled to an adaptor that specifically binds to the probe, rather thanto the probe itself.

In some embodiments, at least two adaptors are used. In one aspect, morethan one probes are delivered to the sample, and at least one adaptor isprovided for each probe that specifically binds to the probe. In oneaspect, one or more adaptors are provided for specifically binding toeach probe. For example, a pair of adaptors is used to specifically bindto the probe 426 and 428, respectively. In certain embodiments, theadaptors of the pair are DNA molecules that: 1) hybridize or otherwisebind to probe 426 or 428; 2) have free 3′ and/or 5′ ends that enable theencoding sequences (e.g., address tags 430 and 432) to be attached in asubsequent step or steps, for example, by ligation; 3) are in a formwhere they can be joined if they are co-localized or in proximity toeach other. In some embodiments, part of probe 426 or 428 acts as asplint to enable ligation, or extension and ligation, of the adaptors inthe adaptor pair. Additional tags (e.g., an address tag, an adaptor forligation, or a universal sequencing primer or amplification primersequence) can be coupled to the adaptor generated by joining the adaptorpair.

FIG. 4B shows an address tagging scheme that may be used for 100 uniquesites in a sample. For example, twenty probe/address tag conjugates a1through a10 and b1 through b10 can be used, with each of a1 through a10corresponding to a probe/address tag conjugate 420 (comprising anaddress tag 408) and each of b1 through b10 corresponding to aprobe/address tag conjugate 422 (comprising an address tag 406). Theaddress tag comprised in each of a1 through a10 and b1 through b10 maybe uniquely identified. Probe/address tag conjugate a1, for example, isdelivered to the biological sample through an addressing channel shownas the first horizontal channel in 412. Probe/address tag conjugate a2is delivered to the biological sample through the second horizontalchannel in 412. Probe/address tag conjugate a3 is delivered to thebiological sample through the third horizontal channel in 412, and soon. Whereas the “a” probe/address tag conjugates are delivered in tenhorizontal channels, the “b” probe/address tag conjugates are deliveredin ten vertical channels as shown in 414. For example, probe/address tagconjugate b1 is delivered to the biological sample through the firsthorizontal channel of 414, probe/address tag conjugate b2 is deliveredto the biological sample through the second horizontal channel of 414,and so on. In other embodiments, the “a” tags may be referred to as the“X” tags and the “b” tags as “Y” tags. The intersections or junctionsbetween the horizontal and vertical channels are shown as solid squares.Each intersection or junction can be uniquely identified by thecombination of the “a” probe/address tag conjugate and the “b”probe/address tag conjugate delivered to the area in the samplecorresponding to the intersection or junction.

FIG. 4C shows a representative tissue section 416 coincident with grid418. The arrows show how the “a” probe/address tag conjugates and the“b” probe/address tag conjugates are delivered on grid 418 that iscoincident with tissue section 416. If, once analyzed, probe/address tagconjugates a1 and b4, e.g., are associated with a target, then thattarget is present in the tissue section at location (a1, b4).

The methods and assay systems disclosed herein are capable ofmultiplexing. For example, FIG. 5 provides an address tagging (or“address coding”) scheme used in a multiplexed assay. For clarity, twoprobes TS01 and TS02, specific for target 1 and target 2, respectively,are shown at 520. FIG. 5 shows address tags 510, comprising a1, a2, a3,a4 and b1, b2, b3 and b4. A delivery or dispensing scheme is shown at530. Like the grid exemplified in FIG. 4, a1 through a4 are delivered tothe sample through horizontal channels, and b1 through b4 are deliveredto the sample through vertical channels. The intersections between thehorizontal and vertical channels are shown as solid squares. Eachintersection can be uniquely identified by the combination of the “a”probe/address tag conjugate and the “b” probe/address tag conjugatedelivered to the area in the sample corresponding to the intersection.

Probes TS01 and TS02 are delivered to the biological sample and allowedto interact with the entire sample. Probes TS01 and TS02 specificallybind to their corresponding targets if the targets are present in thesample. Unbound probes are then removed, for example, by washing.Address tags 510 are then delivered to the biological sample accordingto the spatial pattern shown at 530. The address tags are coupled, forexample, by ligation (or by extension followed by ligation), to probesthat specifically bind to the biological target 1 or biological target 2in the sample. The coupled constructs (or “probe/address tagconjugates”) are then eluted from the biological sample and pooled. Incertain embodiments, sequencing adaptors may be added through, e.g., PCRor ligation, if the sequencing adaptors are not already included in theaddress tags or probe/address tag conjugates. The probe/address tagconjugates are sequenced by, e.g., high throughput or next generationsequencing.

The pool of resulting assay products is shown at 540. For example,presence of the “a1T2b1” product in the pool indicates readout isobtained for TS02 at position (a1, b1) and therefore target 2 isdetected at position (a1, 1). Thus, a sequence readout is obtained foronly TS01 at positions (a4, b1), (a4, b2), (a1, b3), (a2, b3), (a3, b3),(a4, b3) and (a4, b4) (positions shown with horizontal lines in spatialpattern 550), and a sequence readout is obtained for TS02 only atposition (a1, b1) (position shown with vertical lines in spatial pattern550). A sequence readout is obtained for both TS01 and TS02 at positions(a2, b1), (a3, b1), (a1, b2), (a2, b2), and (a3, b2) (positions shownwith cross-hatching in spatial pattern 550). No sequence readout isobtained for either TS01 or TS02 at (a1, b4), (a2, b4) or (a3, b4)(positions shown without shading in spatial pattern 550). Thus, in thebiological sample, target 1 is detected in a large portion of the leftside and at the bottom of the sample, while target 2 is detected only inthe upper left portion of the sample, and neither target is detected inthe upper right portion of the biological sample. The differentialexpression of the two biological targets may be mapped back to thebiological sample and to the biological structures or cell types inthese locations in the biological sample.

In addition to location information, relative abundance of thebiological targets across the multiple sites in the sample can beobtained. For example, if it is found that there are ten times as manya4T1b1 sequences occurring in the data set as compared to a4T1b2sequences, this would indicate that target 1 is ten times more abundantat location (a4, b1) than at location (a4, b2).

In the case of nucleotide analysis as shown in FIG. 3, by ligating theaddress tags directly to the probes, only 2n probes are needed for ntargets. For example, assaying 100 different targets at 10,000 sites ina sample would require 2×100 probes and 2×100 address tags which are tobe coupled to the probes. The total count of assay oligonucleotideswould be only 400 (200 probes and 200 address tags), not countinguniversal primers. In contrast, if the address tags are not decoupledfrom the probes, the total count of assay oligonucleotides would be(n××positions)+(n×Y positions), or in the above example, 20,000oligonucleotides, not counting universal primer sequences. In otherembodiments, for each site in the sample, three, four or more addresstags may be used, and attached to the probes or one another by varyingmeans and in varying combinations of steps.

The methods and assay systems disclosed herein are particularly suitablefor generating a large amount of information with even a modest numberof assays. For example, five or more biological targets assayed at fiveor more positions in the sample generates 25 or more combinations. Usingdigital sequencing as a readout, the optimum number of sequence readsper combination depends on the sensitivity and dynamic range required,and can be adjusted. For example, if for each combination on average 100reads are sampled, the total for 25 combination is 2,500 reads. If 1,000targets are assayed at 1,000 locations with an average sampling depth of1,000, then 10⁹ reads are required. These numbers, although large, arewithin the capacity of intrinsically parallel digital sequencingmethods, which can generate datasets of billions or even trillions ofreads in a reasonable timeframe and at a very low cost per read.Therefore, by varying the numbers of positions or biological targetsassayed, or both, and using digital sequencing, large amounts ofinformation can be obtained. In specific aspects, multiple locations areassayed for two or more biological molecules.

Thus, provided herein is an ability to look at many different biologicaltargets in many locations of a sample at the same time, for example, inthe same reaction run. In some embodiments, the product of the multiplebiological targets being assayed and the multiple sites in thebiological sample is greater than about 20. In other embodiments, theproduct of the multiple biological targets being assayed and themultiple sites in the biological sample is greater than about 50. Inother embodiments, the product of the multiple biological targets beingassayed and the multiple sites in the biological sample is greater thanabout 100, greater than about 500, greater than about 1,000, greaterthan about 10,000, greater than about 25,000, greater than about100,000, greater than about 500,000, or greater than about 1,000,000. Itwill be appreciated that even much larger numbers can be contemplated.For example, assaying 10,000 targets per location for 10,000 locationsin a sample would generate 10⁸ different assays. In some embodiments,sufficient numbers of sites in a sample can be assayed to reach aresolution on the order of that of single cells. Further, in embodimentswhere high-throughput digital sequencing is employed, the sequences ofat least 1,000 probes or probe/address tag conjugates are typicallydetermined in parallel. More typically, using a digital readout, it isdesirable to obtain multiple sequence reads for each assay (defined by atarget and a location, i.e., by the identities of an identity tag and anaddress tag of a target). It is desirable to obtain an average of atleast 3 copies per assay, and more typically at least 10 or at least 30copies per assay, depending on the design of the experiment andrequirements of the assay. For a quantitative readout with suitabledynamic range, it may be desirable to obtain at least 1,000 reads perassay. Therefore, if 1,000,000 assays are carried out, the number ofsequence reads may be 1 billion or more. With high-throughput digitalsequencing, and allowing for redundancy, the sequence of at least 10,000probes or probe/address tag conjugates can be determined in parallel, orthe sequence of at least 100,000, 500,000, 1,000,000, 10,000,000,100,000,000, 1,000,000,000 or more probes or probe/address tagconjugates can be determined in parallel.

In certain aspects, disclosed herein are methods and assay systems forevaluating differences in the amount and/or activity of biologicaltargets between different locations in a sample and/or between samples.In one embodiment, the method comprises evaluating the differences inquantity of the biological targets at each location in the biologicalsample. In another embodiment, the method comprises comparing spatialpatterns of abundance, expression, and/or activity of one or morebiological targets among multiple samples.

Spatially Encoded Protein In Situ Assay

In certain embodiments, it is desirable to correlate spatial patterns ofa target polynucleotide expression, for example, mRNA expressionpatterns within a 2D sample, with histological features of the sample.In certain aspects, the histological features may include the expressionpattern of a known marker for the sample, for example, a tissue-specificmarker, a cell type marker, a cell lineage marker, a cell morphologymarker, a cell cycle marker, a cell death marker, a developmental stagemarker, a stem cell or progenitor cell marker, a marker for adifferentiated state, an epigenetic marker, a physiological orpathophysiological marker, a marker for a transformed state, a cancermarker, or any combination thereof. In certain aspects, the histologicalfeature comprises tissue morphology, for example, as indicate by theexpression pattern of a protein marker. In certain embodiments, in orderto obtain spatial information of the sample, e.g., histological featuresof the sample, expression pattern of a protein marker, and/or tissuemorphology, imaging techniques have to be used. For instance,immunohistochemical (IHC) and/or immunofluorescent (IF) imaging may needto be used.

In certain aspects, provided herein are methods called Spatially EncodedProtein In Situ Assays (SEPIA) for multiplexed in situ analysis ofproteins. In some embodiments, SEPIA and related assay systems canobtain spatial information on the relative abundance of many proteins intissue sections. In certain embodiments, the methods and assay systemsof the present disclosure are based on the use of antibodies (or otheraffinity capture agents capable of specifically binding to a target,other than by nucleotide sequence complementarity) that are labeled withan identity tag that identifies the target protein or the antibody, andone or more address tags that identify the location of each of multiplesites in a sample. In one embodiment, there are provided at least twoaddress tags for each site, one of the at least two address tagsidentifying the location in the tissue section in one dimension (forexample, an X coordinate) and the other identifying the location inanother dimension (for example, a Y coordinate).

In any of the embodiments disclosed herein, the biological target can bea peptide or a protein, and the methods or assay systems can be used toanalyze the presence of antibodies, enzymatic and other proteinactivities, posttranslational modifications, active and non-active formsof peptides, as well as peptide isoforms in a biological sample.Accordingly, the probes may comprise an active region of an enzyme, abinding domain of an immunoglobulin, defined domains of proteins, wholeproteins, synthetic peptides, peptides with introduced mutations,aptamers and the like.

In any of the embodiments disclosed herein, the probes can comprisesubstrates for enzymes or proenzymes, e.g., kinases, phosphatases,zymogens, proteases, or fragments thereof. In certain aspects, theprobes may comprise phosphorylation substrates used to detect proteinsinvolved in one or more signal transduction pathways. In other aspects,the probes can comprise specific protease substrates that associate withspecific individual proteases or specific classes of proteases. In otheraspects, the probes can comprise different processed forms, isoformsand/or domains of an enzyme. In certain embodiments, a protein-basedprobe can be conjugated or otherwise linked to an oligonucleotideaddress tag. In preferred embodiments, the oligonucleotide address tagmay comprise a nucleotide sequence component that allows foridentification of the protein probe.

In preferred embodiments, antibodies that are conjugated tooligonucleotide tags are compatible with the address tagging schemedisclosed herein. In certain aspects, provided herein are methods andassay systems that are highly multiplexed, scalable, and high-throughputfor determining a spatial pattern of abundance, expression, and/oractivity of a target protein across multiple sites in a sample, using anucleic acid readout and independent of imaging for the target protein.In preferred embodiments, provided herein are methods and assay systemsto correlate nucleic acid expression patterns (e.g., DNA or RNAexpression patterns) with cell type-specific protein marker abundancewithout the need for imaging for the protein marker, for example, byimmunohistochemical or immunofluorescent imaging. In preferredembodiments, spatial resolution of the present methods and assay systemsmay approach the scale of individual cells. In certain aspects,correlated 2D and 3D maps of RNA and protein abundance can be generatedusing the present methods and assay systems.

As shown in FIG. 6, in one aspect, a highly multiplexable proteindetection assay is carried out on a sample 616 (shown in FIG. 6C). Inpreferred embodiments, sample 616 preserves the spatial organization ofcells in a tissue. For example, sample 616 can be a paraffin-embedded orfresh-frozen tissue section fixed to a glass slide. FIG. 6A shows twoprobes 620 and 622 specifically bound to a protein target 602 ofinterest. The first probe 620 may comprise target-binding moiety 608,associated with oligonucleotide tag 604. Target-binding moiety 608 andoligonucleotide tag 604 can be conjugated or covalently linked.Target-binding moiety 608 can comprise any affinity capture agents,e.g., antibodies, that specifically bind to protein target 602. Probe620 may further comprise address tag 624 and tag 626. Tag 626 can be auniversal priming site for amplification of the assay products and/or anadaptor to enable identification of the address tag 624 and/oroligonucleotide tag 604 and/or other regions of probe 620, for example,using sequencing technologies. In certain embodiments, tag 626 isconjugated or linked to or otherwise associated with address tag 624,for example, by ligation, extension, ligation followed by extension, orany combination thereof. In one aspect, conjugated, linked or otherwiseassociated tag 626 and address tag 624 as a whole are conjugated orlinked to or otherwise associated with oligonucleotide tag 604. Inalternative embodiments, tag 626 and address tag 624 may be separatelyconjugated or linked to or otherwise associated with probe 620, forexample, at target-binding moiety 608 and/or oligonucleotide tag 604.

Similarly, the second probe 622 may comprise target-binding moiety 606,associated with oligonucleotide tag 610. Target-binding moiety 606 andoligonucleotide tag 610 can be conjugated or covalently linked.Target-binding moiety 606 can comprise any affinity capture agents,e.g., antibodies, that specifically bind to protein target 602. Probe622 may further comprise address tag 628 and tag 630. Tag 630 can be auniversal priming site for amplification of the assay products and/or anadaptor to enable identification of the address tag 628 and/oroligonucleotide tag 610 and/or other regions of probe 622, for example,using sequencing technologies. In certain embodiments, tag 630 isconjugated or linked to or otherwise associated with address tag 628,for example, by ligation, extension, ligation followed by extension, orany combination thereof. In one aspect, conjugated, linked or otherwiseassociated tag 630 and address tag 628 as a whole are conjugated orlinked to or otherwise associated with oligonucleotide tag 610. Inalternative embodiments, tag 630 and address tag 628 may be separatelyconjugated or linked to or otherwise associated with probe 622, forexample, at target-binding moiety 606 and/or oligonucleotide tag 610.

In certain embodiments, target-binding moiety 606 and target-bindingmoiety 608 bind to adjacent sites on target 602, so that two free endsof oligonucleotide tags 604 and 610 are brought close to each other. Inone embodiment, oligonucleotide tags 604 and 610 may be ligated and theligation product assayed. In other embodiments, one or both ofoligonucleotide tags 604 and 610 may be extended and then ligated to theother probe to form an extended probe comprising target target-bindingmoiety 606 and target-binding moiety 608. For example, a DNA ligase maybe added together with a splint to join two free ends of oligonucleotidetags 604 and 610, and the DNA ligated product can serve as the templatedetectable by real-time PCR and/or various sequencing technologies. Sucha dual targeting approach may be used to increase assay specificity.Other aspects and embodiments of the dual targeting approach thatconverts specific protein detection into nucleic acid analysis,including the proximity ligation assay described in Fredriksson et al.,2002, Nat Biotechnol 20, 473-7, may be used in the methods and assaysystems of the present disclosure. It is also within the presentdisclosure that in certain embodiments, target-binding moiety 606 andtarget-binding moiety 608 may bind to different protein targets. Whenthe protein targets are in close proximity, for example, when the twoare in the same complex or brought into contact with each other in areaction, a ligation product may be formed between oligonucleotide tags604 and 610 and detected.

In certain embodiments, a primary antibody and a secondary antibody maybe used. For example, target-binding moiety 606 and/or target-bindingmoiety 608, instead of specifically binding to target 602 directly, mayspecifically bind to a primary antibody that specifically recognizestarget 602. In this case, target-binding moiety 606 and/ortarget-binding moiety 608 may be comprised in a secondary antibody. Incertain aspects, the approach involving a primary antibody and asecondary antibody may be suitable when target expression in low in asample, because one molecule of target 602 may be able to bind multiplemolecules of a primary antibody, thereby amplifying the signal.

In other embodiments, a biological target 632 is assayed according tothe combinatorial address tagging scheme shown in FIG. 6D. Two probes650 and 652 specifically bind to the biological target 632 of interest.In one embodiment, the first probe 650 comprises target-binding moiety638, associated with oligonucleotide tag 634, and the second probe 652comprises target-binding moiety 636, associated with oligonucleotide tag640. Target-binding moiety 638 and oligonucleotide tag 634 (ortarget-binding moiety 636 and oligonucleotide tag 640) can be conjugatedor covalently linked. In particular embodiments, target-binding moiety638 or 636 comprises an affinity capture agent, e.g., an antibody, thatspecifically binds to target 632. In certain embodiments, target 632comprises a protein moiety, an oligosaccharide or polysaccharide moiety,a fatty acid moiety, and/or a nucleic acid moiety. In some embodiments,each probe has a portion that specifically binds to an adaptor 662, forexample, by specific nucleic acid hybridization. In one embodiment,oligonucleotide tag 634 or 640 (or a portion thereof) specificallyhybridizes to the adaptor. The adaptor can specifically bind to thefollowing combinations: 1) the 5′ portion of oligonucleotide tag 634 andthe 3′ portion of oligonucleotide tag 640; 2) the 3′ portion ofoligonucleotide tag 634 and the 5′ portion of oligonucleotide tag 640;3) the 5′ portion of oligonucleotide tag 634 and the 5′ portion ofoligonucleotide tag 640; or 4) the 3′ portion of oligonucleotide tag 634and the 3′ portion of oligonucleotide tag 640. In certain embodiments,oligonucleotide tag 634 or 640 is a linear molecule, a branchedmolecule, a circular molecule, or a combination thereof. After bindingof the two probes to the biological target and the adaptor to the twoprobes, address tags can be delivered to the sample and coupled to theadaptor. For example, the adaptor can be tagged with address tag 654,associated with tag 656, and/or with address tag 658, associated withtag 660. Tags 656 and 660 can be universal priming sites foramplification of the assay products or sequences to enableidentification of the address tags and/or other regions ofadaptor/address tag conjugates, for example, using sequencingtechnologies. In certain embodiments, the address tags are tagged at thesame end of the adaptor, or at different ends of the adaptor. In otherembodiments, an address tag and/or tag 656 or 660 can be pre-coupled tothe adaptor, and the adaptor/address tag or adaptor/tag conjugate orcomplex is then delivered to the sample in order to bind to the probebound to the biological target.

In certain embodiments, all or a portion of the adaptor/address tagconjugate sequence is determined, for example, by nucleic acidsequencing. In other embodiments, all or a portion of theoligonucleotide tag sequence, and/or all or a portion of theadaptor/address tag conjugate sequence, is determined. For example, afirst address tag can be coupled to oligonucleotide tag 634, and asecond address tag can be coupled to adaptor 662. The duplex formedbetween oligonucleotide tag 634 and adaptor 662 can be subjected toextension and sequencing, to generate a conjugate that comprisessequences of the first address tag, all or a portion of oligonucleotidetag 634, all or a portion of adaptor 662, and the second address tag.

The tagging scheme is not limited to the use of two or more probes forthe same biological target. For example, in cases where one probe isused, a tag (e.g., an address tag, an adaptor for ligation, or auniversal sequencing primer or amplification primer sequence) can becoupled to an adaptor that specifically binds to the probe, rather thanto the probe itself.

Additional details of the polynucleotide-protein conjugates used in thepresent disclosure are disclosed in U.S. Provisional Patent ApplicationSer. No. 61/902,105, filed Nov. 8, 2013, entitled “Polynucleotideconjugates and methods for analyte detection,” the disclosure of whichis incorporated by reference in its entirety for all purposes.

In some embodiments, more than one adaptor is used. For example, a pairof adaptors is used to specifically bind the oligonucleotide tag 634 and640, respectively. In certain embodiments, the adaptors of the pair areDNA molecules that: 1) hybridize or otherwise bind to the protein-DNAconjugates, for example, probe 650 or 652; 2) have free 3′ and/or 5′ends that enable the encoding sequences (e.g., address tags 654 and 658)to be attached in a subsequent step or steps, for example, by ligation;3) are in a form where they can be joined if they are co-localized or inproximity to each other. In some embodiments, part of theoligonucleotide portion of probe 650 or 652 acts as a splint to enableligation, or extension and ligation, of the adaptors in the adaptorpair. Additional tags (e.g., an address tag, an adaptor for ligation, ora universal sequencing or amplification primer sequence) can be coupledto the adaptor generated by joining the adaptor pair.

In another embodiment, a method disclosed herein makes it easier tocarry out protein-based assays at the same time as nucleic-acid basedassays. For example, the adaptors can be designed so that they arecompatible with the same encoding oligonucleotides used for thenucleic-acid based assays, e.g., RNA-based assays. Thus, two types ofbinding assays (i.e., detecting a protein target using aprotein-polynucleotide conjugate, and detecting a nucleic acid targetusing a nucleic acid probe) can be carried out in the same reactionvolume or in the same experimental run, and the spatial addressing canbe performed on both types of probes simultaneously.

In yet another embodiment, the present disclosure provides a control forassays detecting a protein target or a biological target comprising aprotein moiety. For example, the nucleic acid portion of theprotein-nucleic acid conjugate is used to hybridize to a nucleic acid inthe sample. This anchors an “artificial” protein (known composition andabundance based on the abundance of the hybridizing sequence) in thesample. The “artificial” protein can then be detected using a number ofmeans, including protein-binding spatially-addressed assays disclosedherein. The approach is not limited to proteins. For example, smallmolecules, such as haptens, can also be used. In one aspect, FIG. 6Eillustrates the general concept of a method of detecting an RNA withknown composition and abundance in the sample, thereby providing acontrol for the detection of other targets (e.g., protein targets) inthe sample. In FIG. 6E, conjugates 662 and 664 each comprises a nucleicacid portion and an antibody-binding portion (circle indicates theantibody-binding portion of conjugate 662, and triangle indicates theantibody-binding portion of conjugate 664). In certain aspects, RNA 666with known composition and abundance in the sample is specifically boundby the nucleic acid portions of conjugates 662 and 664. In someembodiments, the composition and/or abundance of RNA 666 are determinedexperimentally, for example, using a method of the present disclosure,and in specific embodiments, simultaneously with the detection of theprotein target. In other embodiments, the composition and/or abundanceof RNA 666 is derived from prior knowledge or knowledge in the art. Inparticular embodiments, the antibody-binding portions can be HA or FLAG,and the antibody portions of probes 650 and 652 can be an anti-HAantibody or an anti-FLAG antibody, for example, polyclonal or monoclonalantibodies. Other protein-antibody binding pairs are known in the artand can be used in the present disclosure.

FIG. 6B shows an address tagging scheme that may be used for 100 uniquesites in a sample. For example, twenty probes/address tag conjugates X1through X10 and Y1 through Y10 can be used, with each of X1 through X10comprising an address tag 624 and each of Y1 through Y10 comprising anaddress tag 628. The address tag comprised in each of X1 through X10 andY1 through Y10 may be uniquely identified. Probe/address tag conjugateX9, for example, is delivered to the biological sample in the ninthvertical channel in 612. Whereas the “X” probe/address tag conjugatesare delivered in ten vertical channels, the “Y” probe/address tagconjugates are delivered in ten horizontal channels as shown in 614. Forexample, probe/address tag conjugate Y1 is delivered to the biologicalsample in the first horizontal channel of 614. In other embodiments, the“X” tags may be referred to as the “a” tags and the “Y” tags as “b”tags.

FIG. 6C shows a representative tissue section 616 coincident with grid618. The arrows show how the “X” probe/address tag conjugates and the“Y” probe/address tag conjugates are delivered on grid 618 that iscoincident with tissue section 616. If, once analyzed, probe/address tagconjugates X9 and Y1, e.g., are associated with a target, then thattarget is present in the tissue section at location (X9, Y1).

Any suitable configuration of the oligonucleotide/antibody (or othertarget-specific binder) conjugate may be used to convert specificprotein detection into nucleic acid analysis. In certain embodiments,for example, as shown in FIG. 7A, probe 708 specifically binds toprotein target 702. Probe 708 may comprise target-binding moiety 704,associated with oligonucleotide tag 706. Target-binding moiety 704 andoligonucleotide tag 706 can be conjugated or covalently linked.Target-binding moiety 704 can comprise any affinity capture agents,e.g., antibodies, that specifically bind to protein target 702. Probe708 may further comprise “X” address tag 710 and “Y” address tag 712.Both address tags 710 and 712 may be conjugated to a universal primingsite for amplification of the assay products and/or an adaptor (notshown in FIG. 7) to enable identification of the address tags 710 and712 and/or oligonucleotide tag 706 and/or other regions of probe 708,for example, using sequencing technologies. Conjugation of the varioustags may be accomplished by ligation, extension, ligation followed byextension, or any combination thereof. In some embodiments, address tags710 and 712 are conjugated to one side of oligonucleotide tag 706 or theother (i.e., 5′ or 3′ of the sequence), respectively. In alternativeembodiments, both address tags 710 and 712 may be conjugated to either5′ or 3′ of oligonucleotide tag 706. For example, address tags 710 and712 may be directly or indirectly conjugated, and address tag 710 or 712may be directly or indirectly conjugated to either 5′ or 3′ ofoligonucleotide tag 706.

In other embodiments, for example, as shown in FIG. 7B, probe 720specifically binds to protein target 714. Probe 720 may comprisetarget-binding moiety 716, conjugated, linked, or otherwise associatedwith oligonucleotide tag 718. Target-binding moiety 716 can comprise anyaffinity capture agents, e.g., antibodies, that specifically bind toprotein target 714. Probe 720 may further comprise oligonucleotidesequence 722 that specifically hybridizes to oligonucleotide tag 718. Inone embodiment, sequence 722 is complementary to oligonucleotide tag718. Sequence 722 may be conjugated to “X” address tag 724 and “Y”address tag 726. Both address tags 724 and 726 may be conjugated to auniversal priming site for amplification of the assay products and/or anadaptor (not shown in FIG. 7) to enable identification of the addresstags 724 and 726 and/or sequence 722 and/or other regions of probe 720,for example, using sequencing technologies. Conjugation of the varioustags may be accomplished by ligation, extension, ligation followed byextension, or any combination thereof. Similar to FIG. 7A, address tags724 and/or 726 can be conjugated to either side of oligonucleotidesequence 722 (i.e., 5′ or 3′ of the sequence), either directly orindirectly.

In further embodiments, for example, as shown in FIG. 7C, a “2-antibody”format may be used. The “2-antibody” format is similar to the dualtargeting approach discussed above, for example, in FIG. 6. In thisembodiment, two antibodies specific for a protein target are conjugatedto an oligonucleotide, which can be directly or indirectly conjugated tothe “X” and “Y” address tags and a universal priming site foramplification of assay products and/or an adaptor for sequencing. Insome embodiments, the two antibodies may bind to different epitopes orsites on the protein target. In preferred embodiments, binding of bothantibodies to the target is required to generate a signal, thusproviding higher specificity than using only one antibody. It is alsocontemplated that more than two antibodies may be conjugated to anoligonucleotide and used in the methods and assay systems of the presentdisclosure.

As disclosed herein, the methods and assay systems permit high levels ofmultiplexing. In one embodiment, the probes can be delivered over theentire surface of a 2D sample in a bulk process, and then address taggedby delivering the address tags in a spatially defined pattern. Forexample, two sets of address tags (the “X” and “Y” tags) can be used ina combinatorial fashion as discussed supra. Once the in situ assay iscompleted, the assay products are eluted and sequenced. The address tagsequence information identifies the location at which the assay isperformed, and the probe sequence information (the identity tag)identifies the protein that is targeted. In one aspect, the frequency ofa particular assay product (for example, a sequencing product) in thedigital readout can be used to infer the relative abundance of itstarget in the sample. This information can then be associated with otherinformation, including conventional histological information, and/ortranscript abundance obtained via the related Spatially Encoded GenomicAssays (SEGA). In preferred embodiments, the methods and assay systemsdo not depend on imaging techniques for the spatial information of thetarget protein. Instead, in preferred embodiments, the spatial patternof the target protein abundance, expression, and/or activity can bedetermined by sequencing.

In one embodiment, in order to integrate the protein and gene expressionassays, the same address tagging scheme is compatible with and can beused for both assay types. For example, for each of multiple sites in asample, the same combination of “X” and “Y” address tags can be taggedto an antibody-DNA conjugate for a target protein, and to a probe for atarget polynucleotide sequence. In one embodiment, the targetpolynucleotide or the complement thereof encodes all or a portion of thetarget protein. Therefore, for each site in the sample, the abundance,expression, and/or activity of the target protein and its correspondingpolynucleotide can be detected by assaying for sequencing products withthe same set of address tags. In preferred embodiments, the step ofanalyzing probes or probe/address tag conjugates bound to the targetprotein and the step of analyzing probes or probe/address tag conjugatesbound to the target polynucleotide can be performed in parallel in thesame reaction run. In alternative embodiments, different address tagsmay be coupled to an antibody-DNA conjugate for a target protein, and toa probe for a target polynucleotide sequence, to determine theabundance, expression, and/or activity of the target protein and thetarget polynucleotide at a given site. Assay results for the targetprotein and the target polynucleotide can then be integrated for eachsite in the sample.

Various methods can be used to form an amplifiable construct, forexample, by using ligation of proximal probes followed by sequentialligation of a pair of spatial encoding adaptors (address tags) as shownin FIG. 8A. In one embodiment, two DNA probes are hybridized proximal toone another on an RNA target (or template). The probes are subsequentlyligated to one another and the quantity of the ligated pair is taken asa measure of the amount of the target present in the sample. In certaincases, however, the efficiency of T4 DNA ligase is reduced when theligation reaction occurs on an RNA template as compared to a DNAtemplate. In other cases, the ligation efficiency is dependent on thesequence of the DNA probes that are being joined, the particularly onthe identity of the first few bases on either side of the junction. Insome embodiments, a method disclosed herein mitigates both problems.FIG. 8B shows the general principle of the method. In this case, insteadof using probes that hybridize in direct proximity on an RNA target, theprobes are separated by some distance with non-hybridizing overhangingsequences on their proximal ends. These overhanging sequences aredesigned to be complementary to a short DNA splint. This splint can beuniversal for all the probe pairs in a multiplexed assay or can bespecific for a given probe pair or subset of probe pairs. The distancebetween the two probes in a pair can be adjusted to optimize ligationefficiency. There is flexibility in this distance, which provides anadditional degree of freedom when designing probes versus the use ofproximal probes. Once the probes are hybridized to the RNA target,excess probes are washed away. The splint is hybridized to theoverhanging regions at the proximal ends of the probes, and the probesare joined by enzymatic ligation. After ligation, the remaining steps ofthe assay are performed, for example, ligating the spatial encodingadaptors to each end of the ligated probe pair. In certain aspects,since DNA splinted ligation is more efficient than RNA splintedligation, a method disclosed herein improves the efficiency at which thetwo probes are joined. In addition, using a universal splint eliminatesthe sequence-dependent variation in ligation efficiency between themultiple probe sets in a multiplexed in situ assay. In another aspect,probes can be more easily designed, and more suitable probe sets can bedesigned, due to increased freedom of varying the distance betweenprobes.

Reagent Delivery Systems

The reagent delivery system of the present disclosure includesinstrumentation that allows the delivery of reagents to discreteportions of the biological sample, maintaining the integrity of thespatial patterns of the addressing scheme. Reagent delivery systems ofthe present assay systems comprise optional imaging means, reagentdelivery hardware and control software. Reagent delivery can be achievedin a number of different ways. It should be noted that reagents may bedelivered to many different biological samples at one time. A singletissue section has been exemplified herein; however, multiple biologicalsamples may be manipulated and analyzed simultaneously. For example,serial sections of a tissue sample can be analyzed in parallel and thedata combined to build a 3D map.

Integral to the assay system of the present disclosure isinstrumentation that allows for spatial patterning of reagents onto thebiological sample. Technologies for formulating and delivering bothbiological molecules (e.g., oligonucleotides or antibodies) and chemicalreagents (e.g., small molecules or dNTPs) are known in the art, and usesof these instrument systems are known to one skilled in the art andeasily adaptable to the assay systems of the present disclosure. Oneexample of a suitable reagent delivery system is the Labcyte™ Echoacoustic liquid handler, which can be used to deliver nanoliter scaledroplets containing biological molecules with high precision andreproducibility. One skilled in the art could incorporate this reagentdelivery device into the overall system using software to specify thelocations to which reagents should be delivered.

Other instruments that can be used for the delivery of agents and/orcoding identifiers onto biological samples include, but are not limitedto, ink jet spotting; mechanical spotting by means of pin, pen orcapillary; micro contact printing; photochemical or photolithographicmethods; and the like. For several applications, it may be preferred tosegment or sequester certain areas of the biological samples into one ormore assay areas for different reagent distributions and/or biologicaltarget determination. The assay areas may be physically separated usingbarriers or channels.

In one exemplary aspect, the reagent delivery system may be a flow-basedsystem. The flow-based systems for reagent delivery in the presentinvention can include instrumentation such as one or more pumps, valves,fluid reservoirs, channels, and/or reagent storage cells. Reagentdelivery systems are configured to move fluid to contact a discretesection of the biological sample. Movement of the reagents can be drivenby a pump disposed, for example, downstream of the fluid reagents. Thepump can drive each fluid reagent to (and past) the reactioncompartment. Alternatively, reagents may be driven through the fluid bygravity. US Pub. Nos. 20070166725 and 20050239192 disclose certaingeneral purpose fluidics tools that can be used with the assay systemsof the present disclosure, allowing for the precise manipulation ofgases, liquids and solids to accomplish very complex analyticalmanipulations with relatively simple hardware.

In a more specific example, one or more flow-cells can be attached tothe substrate-affixed biological sample from above. The flow-cell caninclude inlet and outlet tubes connected thereto and optionally anexternal pump is used to deliver reagents to the flow-cell and acrossthe biological sample. The flow cells are configured to deliver reagentsonly to certain portions of the biological sample, restricting theamount and type of reagent delivered to any specific section of thebiological sample.

In another aspect, a microfluidic system can be integrated into thesubstrate upon which the biological sample is disposed or externallyattached on top of the substrate. Microfluidic passages for holding andcarrying fluid may be formed on and/or above the planar substrate by afluidics layer abutted to the substrate. Fluid reagents can be selectedand delivered according to selective opening and closing of valvesdisposed between reagent reservoirs.

Pumps generally include any mechanism for moving fluid and/or reagentsdisposed in fluid. In some examples, the pump can be configured to movefluid and/or reagents through passages with small volumes (i.e.,microfluidic structures). The pump can operate mechanically by exertinga positive or negative pressure on fluid and/or on a structure carryingfluid, electrically by appropriate application of an electric field(s),or both, among other means. Exemplary mechanical pumps may includesyringe pumps, peristaltic pumps, rotary pumps, pressurized gas,pipettors, etc. Mechanical pumps may be micromachined, molded, etc.Exemplary electrical pumps may include electrodes and may operate byelectrophoresis, electroendosmosis, electrocapillarity,dielectrophoresis (including traveling wave forms thereof), and/or thelike.

Valves generally include any mechanism for regulating the passage offluid through a chatmel. Valves can include, for example, deformablemembers that can be selectively deformed to partially or completelyclose a channel, a movable projection that can be selectively extendedinto a channel to partially or completely block a channel, anelectrocapillary structure, and/or the like.

An open gasket can be attached to the top of the biological sample andthe sample and reagents can be injected into the gasket. Suitable gasketmaterials include, but are not limited to, neoprene, nitrile, andsilicone rubber. Alternatively, a watertight reaction chamber may beformed by a gasket sandwiched between the biological sample on thesubstrate and a chemically inert, water resistant material such as, butnot limited to, black-anodized aluminum, thermoplastics (e.g.,polystyrene, polycarbonate, etc.), glass, etc.

Microfluidic devices that can be used in the methods and systems of thepresent disclosure are disclosed in detail in U.S. Application Ser. No.61/839,320, filed Jun. 25, 2013, entitled “Spatially encoded biologicalassays using a microfluidic device,” and in International ApplicationNo. PCT/US2014/44191, filed Jun. 25, 2014, entitled “Spatially encodedbiological assays using a microfluidic device,” the disclosures of whichare incorporated herein in their entireties by reference for allpurposes.

In an optional embodiment, the assay system comprises imaging means todetermine features and organization of the biological sample ofinterest. The images obtained, e.g., may be used to design the deliverypattern of the reagents. Imaging means are optional, as an individualcan instead view the biological sample using, e.g., a microscope,analyze the organization of the biological sample, and specify a spatialpattern for delivery assay reagents. If included, the delivery systemcan comprise a microcircuit arrangement including an imager, such as aCCD or IGFET-based (e.g., CMOS-based) imager and an ultrasonic sprayerfor reagent delivery such as described in US Pub. No. 20090197326, whichis incorporated herein by reference. Also, it should be noted thatalthough an X-Y grid configuration is illustrated herein, otherconfigurations can be used, such as, e.g., following the topology of atissue sample; targeting certain groups of cells, cell layers and/orcell types in a tissue, and the like.

In yet another alternative, the reagent delivery system controls thedelivery of reagents to specific patterns on a biological sample surfaceusing semiconductor techniques such as masking and spraying. Specificareas of a biological sample can be protected from exposure to reagentsthrough use of a mask to protect specific areas from exposure. Thereagents may be introduced to the biological sample using conventionaltechniques such as spraying or fluid flow. The use of masked deliveryresults in a patterned delivery scheme on the substrate surface.

In one aspect, the reagent delivery instrumentation is based on inkjetprinting technology. There are a variety of different ink jettingmechanisms (e.g., thermal, piezoelectric) and compatibility has beenshown with aqueous and organic ink formulations. Sets of independentlyactuated nozzles can be used to deliver multiple reagents at the sametime, and very high resolutions are be achieved.

In order to target specific sites of interest, an informative image ofthe biological sample to be assayed may be used to assist in the reagentdelivery methods and associated encoding scheme. Sample regions of thebiological sample can be identified using image processing (e.g., imagesof cell types differentiated by immunohistochemistry or other stainingchemistries) integrated with other features of the assay system. In someaspects, software is used to automatically translate image informationinto a reagent delivery pattern. In some embodiments, a mechanism toregister and align very precisely the biological sample for reagentdelivery is an important component of the assay systems. Mechanisms suchas the use of fiducial markers on slides and/or other very accuratephysical positioning systems can be adapted to this purpose.

The present methods and assay systems may comprise a complete suite ofsoftware tailored to the methods or assay systems. Optionally,oligonucleotide design software is used to design the encodingnucleotides (and in embodiments where nucleic acids are assayed, thetarget-specific oligonucleotides) for the specific assay to be run, andmay be integrated as a part of the system. Also optionally, algorithmsand software for reagent delivery and data analysis (i.e., sequenceanalysis) may be integrated to determine assay results. Integrated dataanalysis is particularly useful, as the type of dataset that isgenerated may be massive as a consequence of scale. Algorithms andsoftware tools that are specifically designed for analysis of thespatially-associated data generated by the assay systems, includingpattern-analysis software and visualization tools, enhance the value ofthe data generated by the assay systems.

In certain aspects, the assay system comprises processes for making andcarrying out the quality control of reagents, e.g., the integrity andsequence fidelity of oligonucleotide pools. In particular, reagents areformulated according to factors such as volatility, stability at keytemperatures, and chemical compatibility for compatibility with thereagent delivery instrumentation and may be analyzed by instrumentationintegrated within the assay system.

Applications of Assay System

It will be apparent to one skilled in the art upon reading the presentdisclosure that there are numerous important areas of biologicalresearch, diagnostics, and drug development that will benefit from ahigh throughput multiplexed assay system that can measure simultaneouslythe amount and spatial location of a biological target in a biologicalsample. For example, combining the ability to estimate the relativeabundance of different RNA transcripts with the ability to reconstructan image of spatial patterns of abundance across many locations, whichmay be as small as or even smaller than individual cells, in a tissueenables many different areas of basic research. The following areexemplary uses and are by no means meant to be limiting in scope.

In one embodiment, the assay systems and devices disclosed herein candiscriminate different tissue types on the basis of tissue-specificdifferences in gene expression. In one aspect, the assay systems anddevices disclosed herein can be used to assay and discriminate mRNA andhnRNA, and therefore can be used for parallel analysis of RNA processingin situ. In one aspect, probes are designed to target introns and/orexons. In one aspect, intronic probes give signal from hnRNA, but notfrom mRNA. The gDNA background signal can be measured using selectivepretreatments, with DNase and/or RNase. In one aspect, splice-sitespecific probes that are selective for spliced RNAs may be designed andused. In certain embodiments, a combination of intronic probes, exonicprobes, and/or splice-site specific probes may be used to identify therelative level of processing intermediates and their differences betweendifferent cells in a tissue section. In general, RNA may be bound toproteins of various types, and hnRNA, in particular, is complexed withproteins to form hnRNP (heterogeneous nuclear ribonucleoprotein). In oneembodiment, the devices and assay systems disclosed herein can be usedto perform highly parallel in situ footprinting experiments. In certainaspects, instead of targeting 1,000 different RNAs, probes can be tileddensely through a smaller number of RNAs in order to generate a signalprofile along the molecule. Relative changes in this profile betweencell types would then indicate differences in availability of the RNA,at the specific locations assayed.

In one example, 3-dimensional patterns of gene expression are determinedby analyzing a series of tissue sections, in a manner analogous to imagereconstruction in CT scanning. Such a method can be used to measurechanges in gene expression in disease pathology, e.g., in canceroustissue and/or a tissue upon injury, inflammation, or infection. With theassay systems of the invention, more detailed information on geneexpression and protein localization in complex tissues is obtained,leading to new insights into the function and regulation both in normaland diseased states, and provides new hypotheses that can be tested. Forexample, an assay system of the invention may enable some of theinsights gained from many individual studies and larger programs likeENCODE (Birney, et al., Nature, 447:799-816 (2007)) and modENCODE to beintegrated at the tissue level. The assay systems also aid computationalefforts to model interacting networks of gene expression in the field ofsystems biology.

The assay systems also provide a novel approach to analysis of somaticvariation, e.g., somatic mutations in cancer or variability in responseto infectious organisms. For example, tumors are typically highlyheterogeneous, containing cancer cells as well as genetically normalcells in an abnormal local environment. Cancer cells undergo mutationand selection, and in this process it is not unusual for local clones todevelop. Identifying relatively rare somatic mutations in the context oftumors may enable the study of the role of key mutations in theselection of clonal variants. Transcriptional patterns associated withangiogenesis, inflammation, or other cancer-related processes in bothcancer and genetically normal cells can be analyzed for insights intocancer biology and assist in the development of new therapeutic agentsfor the treatment of cancers. In another example, individuals havevarying susceptibility to infectious organisms, and the assay systems ofthe invention can be used to study the interaction between microbes andtissues or the various cell types within the tissue.

Importantly, in addition to providing spatially-associated information,the invention allows a great increase in the sensitivity of detectingrare mutations, as signal to noise can be dramatically increased sinceonly a small location is assayed in any given reaction. In a typicalassay for rare mutations in a mixed sample, the sample is treated inbulk, i.e., nucleic acids are extracted from many cells into a singlepool. Thus, if a mutation is present in one cell in 10,000, it must bedetected against a background of normal DNA from 10,000 cells. Incontrast, with the assay systems of the invention many cells can beanalyzed, but individual cells or small groups of cells would beidentified by the spatial coding system. Therefore, in the assay systemsof the present invention, background is reduced by orders of magnitude,greatly increasing sensitivity. Furthermore, the spatial organization ofmutant cells can be observed, which may be particularly important indetecting key mutations in tissue sections in cancer. Already molecularhistological analyses are yielding insights into cancer biology and mayhave potential for use in diagnostics. The technology of the inventionpromises to greatly increase the power of such approaches.

The following exemplary embodiments and examples are intended to furtherdescribe and illustrate various aspects of the invention, but not tolimit, the scope of the invention in any manner, shape, or form, eitherexplicitly or implicitly.

EXAMPLE 1 Proof of Concept of the Addressing Scheme and Scalability

A model system was developed using a microarray to demonstrate a workingmultiplexed spatially encoded abundance assays for polynucleotidetargets. The basic design validates the concept of the assay, and theaddressing scheme, and establishes a working assay prior to addressingissues related to the analysis of a more complicated biological sample.

A microarray was used as a proxy for a tissue section. The targetsequences of the microarray were fully specified, so that thecomposition of the targets was known and was varied systematically,simplifying analysis by next-generation sequencing. One of skill in theart would appreciate that similar assays can be performed on varioussamples including tissue sections, and for various targets includingpolynucleotide or protein targets, as well as other biological targets,according to the present disclosure.

A 16-Plex×8-Site Assay Using 8-Section Microarray as Artificial Sample

This 16-plex×8-site assay was performed using a custom DNA microarray(Agilent) as an artificial sample. Eight sites were used because of thecommercial availability of 8-section microarrays. Sixteen differenttarget sequences were each assayed over a 128-fold range in DNA amount.Differences in DNA amount were obtained by varying the surface area overwhich each sequence was synthesized. Differences in DNA amount weredetected over the entire range for all sixteen targets, usingnext-generation sequencing as the readout. This example demonstrated aworking multiplex assay using a microarray as an artificial sample, andthe spatial encoding accuracy for the model system.

EXAMPLE 2 A Demonstration of Spatial Encoding Using a Spotted Microarray

Scalability of both the spatial addressing and assay systems isdemonstrated by carrying out a 24-plex×24-site assay using a microarraymodel system.

The amount of biological target, here a DNA target sequence, at eachassay location is systematically varied on the microarray substrate. Forexample, in a microarray with 50 micron spot size (center to center), a1 mm² area contains ˜400 spots. The region around each site isoptionally occupied by a region that is devoid of these spots to allowindividual resolvability of the target sequences. Alternatively, thespots may be clustered, with two or more directly adjacent spotssurrounded by or adjacent to a region that is devoid of targetsequences.

In order to demonstrate that spatial addressing or encoding is accurate,the sites comprise different target compositions to show that the assayreadout matches the expected composition of each site. With 24 targetsequences, a simple digital pattern is made with each site having adifferent set of 12 targets present and 12 targets absent, to make abinary code (0=absent, 1=present). The assay readout is then determinedto show that the detected regions match the expected signal afterspatial decoding. In this particular example, the code (address tag)space is large enough (2{circumflex over ( )}24) so that even a fewerrors would not result in different codes being mixed up. Moreover,this design allows identification of errors and allows estimation notonly of accuracy of spatial encoding but also of accuracy calling thepresence or absence of target sequences.

The ability to detect quantitative differences is evaluated bygenerating dose-response curves for each of the 24 assays that arecarried out at each site in a 24-site assay. This allows estimation ofthe limit of detection, dynamic range, and power to detect a givenfold-change across the range.

In one aspect, a latin square design is used to represent individualtargets at different ratios by varying the number of features for eachtarget. In other words, with multiple spots in a site, the number ofspots allocated to each of the 24 target sequences can be varied andeach of the 24 sites can have a different composition. A 1×3 inchmicroarray is sufficiently large to permit multiple replicates. Thislarger set of 24 sequences will require deconvolution, and this isaccomplished by using high throughput techniques such as next-generationsequencing technologies (e.g., SOLiD™ technology (Life Technologies,Inc., Carlsbad, Calif.) or Genome Analyzer (Illumina, Inc., San Diego,Calif.)). The use of the 24-plex assay demonstrates both the accuracy ofspatial encoding and decoding, and the quantitative response of theassay system.

EXAMPLE 3 Assays for Preserved Samples and Biological Samples

Genomic DNA is assayed in order to characterize variation in coding andregulatory sequences, such as single nucleotide polymorphisms (SNPs) ormutations, small insertions and deletions (indels), copy number variantssuch as gene deletions or amplifications, and genetic rearrangementssuch as translocations, all of which may be functionally significant incancer and other diseases. Genomic sequence variation as a function ofposition in the sample may indicate somatic mosaicism in the sample. Incancer samples, mutations may provide prognostic or diagnostic markersthat may be useful in determining the best course of treatment.Mutations may identify regions of the sample that contain cancer cellsand assist in distinguishing them from normal cells, or cells in thetumor microenvironment that are genetically normal at the sequence levelbut perturbed in other ways as a result of the influence of cancercells. In order to distinguish signal generated from DNA targets fromthose generated by RNA targets, probes can be designed to hybridize tonon-coding sequences that are not transcribed. Alternatively, or inorder to confirm the specificity of DNA targeting, RNA may be degradedby treatment with RNase. Genomic DNA is also assayed in order to obtaininformation about its organization and to provide information on thestate of activation of certain genes. For example, the ability of probesto bind to DNA may be used as an indicator of whether DNA is condensedor otherwise inaccessible, or whether DNA is in an open conformation fortranscription. This type of determination can benefit from comparativeanalysis of samples in which genes are differentially active. Similarlyit may be useful to relate information about RNA and/or proteinabundance to information about the activation state of genes. Othertypes of information are obtained from analysis of epigenetic markersassociated with genomic DNA, such as methylation state and the presenceof histones and other proteins and modifications.

The handling of small absolute numbers of product molecules generatedfrom very small or compromised samples are enhanced to counter the issueof low recovery efficiency; that is, elution is efficient and lossesresulting from adsorption of molecules to surfaces are prevented. Anapproach to addressing the latter issue is to include a carriermaterial, such as glycogen or carrier nucleic acids.

In order to adapt the assay to a biological sample and make the tissuesection RNA assays as informative as possible, pre-existing informationon expression levels in specific tissues to target transcripts across arange of abundances are used in the assay design. Both high abundancetranscripts, as well as some medium and low abundance transcripts, aretargeted to enable an initial assessment of the quantitative performancecharacteristics of the assay. In this assay, a control RNA template isimmobilized to a solid support in order to create an artificial system.The assay is performed using T4 DNA ligase, which can repair nicks inDNA/RNA hybrids. Assays are carried out on matched slides, or differentsections of the same slide, where in one case gDNA is assayed and in theother RNA is assayed. When assaying gDNA the slide can be pretreatedwith RNase, and when assaying RNA the slide is pretreated with DNase.Results of the assay are confirmed by extracting gDNA or RNA andquantitating the relative amounts by qPCR or RT-qPCR, respectively.

EXAMPLE 4 Multiplex Spatially Encoded Polynucleotide Abundance Assays

This example describes representative multiplex spatially encodedabundance assays for polynucleotide targets. One of skill in the artwould appreciate that similar assays can be performed for proteintargets, as well as other biological targets, according to the presentdisclosures.

A 57-Plex Assay Using Formalin-Fixed, Paraffin-Embedded (FFPE) Samples

A scheme using ligation of proximal probes followed by sequentialligation of a pair of spatial encoding adaptors (address tags) was usedto form an amplifiable construct. For example, as shown in FIG. 8A, twotarget-specific probe oligos were ligated together following in situhybridization. A unique adaptor or address tag encoding the X positionwas introduced via a microfluidic channel and ligated to the 5′ end ofthe probes. A second address tag encoding the Y position was similarlyinstalled to the 3′ end of the probes. The address tags containeduniversal priming sites that allowed installation of additionalsequencing adaptors via PCR. The final construct is a substrate fornext-generation sequencing.

A 57-plex assay was performed using a pool of probes for 57 targets oncommercially sourced FFPE sections of normal human liver and pancreas(Pantomics). The pool included probes for 18 liver specific targets, 19pancreas specific targets, 4 housekeeping targets, 6 custom-generatednegative controls sequences, and 10 pluripotency markers. Allliver-specific probes were strongly enriched in liver and all but 3 ofthe pancreas-specific probes were strongly enriched in pancreas. These 3probes had very few total counts so it is likely that they weresequences that hybridized or ligated inefficiently and thus were notreporting accurately. The results of this assay were consistent withpublished data for expression in normal liver and pancreas (BioGPS,available at biogps.org/#goto=welcome).

A number of different reagent delivery technologies, includingrandom-access methods such as inkjet and pin-spotting, can be used forthe multiplex assays. A system using microfluidic flow-channel deviceswas chosen for several reasons. First, soft-lithographic techniquesallow rapid development of such devices at a fraction of the cost andtime needed to develop or buy a suitable instrument for printing orspotting reagents. Second, the size of the sampling area can be strictlydefined using microfluidic devices, whereas printed droplets of reagentwould likely spread non-uniformly on the surface of an FFPE sample andyield sampling areas of varying size and shape. Third, the reagentdelivery system using microfluidic devices does not require precisealignment of the sample. This feature allows sequential ligation of thetwo encoding positional adaptors (i.e., the two address tags). Comparedto simultaneous ligation of the two address tags, sequential ligationminimizes the formation of undesired products. For reagent deliverytechnologies using inkjet or pin-spotting, the location of each dropletor spot of the first address tag must coincide with a droplet or spot ofthe second address tag in order to form the full construct duringsequential ligation. This would require that precise registration of thesample be preserved throughout both printing steps. In contrast, themicrofluidic device based method and system uses a pair of microfluidicdevices each having a set of parallel channels, where the first andsecond devices have their channels oriented perpendicular to one anotheras shown in FIG. 9A.

A microfluidic addressing device is shown with overlayed layout for apair of addressing devices in FIG. 9A, a poly(dimethylsiloxane) (PDMS)elastomer device with 16×16 channels and 100 μm channel width in FIG.9B, and an assembled device with the clamp and peristaltic pumpmechanism in FIG. 9C.

The geometry of the devices defines a rectangular array of junctions,each having an area that is defined by the width of the two channels. Ifeach channel receives a different address tag, the result is a uniquepair of identifying address tags for each junction or intersection inthe array. Fluid flow in microfluidic devices is usually driven byexternal syringe pumps or vacuum and often requires a complex plumbingsetup including connections between the microscopic channels and themacroscopic components of the system. The reagent delivery system usedin the example is a self-contained system for loading reagents into thechannels. The device is cast out of a PDMS elastomer and includesreagent reservoirs, and microscopic addressing channels, each of whichis connected to a larger peristaltic pump channel. The device is appliedto the surface of an FFPE sample and clamped in place. A thumb-wheel isapplied across all the pump channels and the rolling action draws theliquid from each reservoir through the addressing channel where itcontacts the tissue sample and the address tag is ligated onto thehybridized probes. After the first ligation, the device is removed andthe sample washed. The second, perpendicular device is used to installthe second set of address tags. Only the probes under the area at theintersection of two channels receive both address tags. The devices canbe cleaned and reused.

A set of microfluidic devices with a 5-site×5-site layout wasfabricated, to match a set of custom-designed tissue microarrays (TMAs)that contained a corresponding 5×5 checkerboard pattern was produced.The TMAs contained the same commercially sourced FFPE sections of normalhuman liver and pancreas (Pantomics) used above in this example,arranged in a checkerboard pattern. This known pattern of tissue spotson the array was used to verify the accuracy of the spatial encodingsystem. FIG. 10 shows an immunofluorescence image of a TMA as well asexpression maps generated by the assay system using the microfluidicreagent delivery system. FIG. 10A shows immunofluorescence (IF) image ofa custom TMA stained with two liver specific antibodies: PYGL, specificto hepatocytes and Annexin A2, specific to bile-duct cells. Thereference was Protein Atlas, available at www.proteinatlas.org. Thebrightly stained spots are liver tissue and dim spots are pancreas. FIG.10B shows a map of the sum of the 22 most abundant liver-specific genesby abundance, normalized to housekeeping genes (GAPDH and ActB). Eachsquare corresponds to the signal mapped to one junction, a 500 μm×500 μmarea centered on one of the tissue cores of the TMA. FIG. 10C shows amap of the sum of the 22 most abundant pancreas genes by abundance,normalized by housekeeping genes. The addressing channels of themicrofluidic devices used are 500 μm wide at a 2 mm pitch with a depthof 50 μm, which corresponds to a “virtual-volume” of 12.5 nL thatencompasses the intersection of the perpendicular channels.

These results demonstrate that mapped sequencing data using themultiplex system reproduced the expected expression pattern of thetissue sample, and that the multiplex assay is compatible withimmunofluorescence imaging, allowing the determination of cell typesbased on protein markers and correlation with gene expression data.

A 134-Plex Assay Using Formalin-Fixed, Paraffin-Embedded (FFPE) Samples

A probe pool and two device layouts were developed. The probe poolconsisted of 134 targets representing 69 unique genes shown in Table 1.When reading out expression by sequencing, a few highly expressed genescan account for the majority of the reads, limiting dynamic range of theassay. This issue was mitigated by attenuating some of the most highlyexpressed genes in the pool. This was accomplished by adding inattenuator probes in known ratios with the active probes. An attenuatorprobe lacks a 5′ phosphate necessary for ligation, preventing productionof an amplifiable product and thus decreasing the signal from thattarget. Table 2 shows the results of attenuation of the top 5 genes.Before attenuation they accounted for 73% of the reads whereasafterwards they accounted for less than 18%. This strategy can be usedto achieve very high levels of multiplexing with current sequencingtechnology while still achieving high dynamic range.

TABLE 1 List of genes and number of unique targets per gene in 134-plexprobe pool. Pluripotency Liver Liver Pancreas Pancreas AURKB 3 AGXT 2KRT19 2 AQP8 2 DPEP1 2 HMGB3 2 ALDO 2 KRT7 2 CARS 2 GP2 2 JARID2 3 APOB2 MCAM 2 CEL 2 PRSS1 2 LIN28A 1 BHMT 2 MYH9 2 CLPS 2 SOX9 2 SOX2 1 CPB22 POGZ 2 CPA1 2 WDR38 2 Housekeeping CYP2A6 2 SMARCA4 2 GCG 2 ASB9 2ACTB 2 CYP2C8 2 ALB 2 INS 1 CHGA 2 GAPDH 2 HPX 2 ARG1 2 PNLIP 2 GAD2 2H2AFX 2 SAA4 2 CD14 2 PNLIPRP2 2 INSM1 2 Controls SERPIND1 2 MBL2 2PPP4C 2 NCAM1 2 18S 3 VTN 2 PYGL 2 REG1B 2 PAX6 2 Rand Neg 3 CA9 2SLC27AS 2 SEL1L 2 PPY 2 Other EPB41L2 2 STOM 2 CA12 2 SV2A 2 FXR1 2HNF1B 2 CPA2 2 UCHL1 2

TABLE 2 Attenuation of top 5 assay targets Probe Fraction of ReadsAtten. Name w/o Atten. w/ Atten. Factor PNLIP_2 0.253 0.048 5.268PNLIP_1 0.203 0.035 5.871 PRSS1_2 0.114 0.034 3.343 CPA1_2 0.111 0.0234.841 CLPS_2 0.051 0.037 1.373 Sum 0.732 0.177

EXAMPLE 5 Elution and Preparation of Spatially Encoded Probes for NextGeneration Sequencing

Using the methods described supra, a 134-plex pool of probe pairs washybridized to an FFPE sample, ligated and spatially encoded withX-positional and Y-positional adaptors. In preparation for elution, ahybridization chamber (Agilent) was applied to the slide and clamped inplace to form a leakproof chamber containing the FFPE tissue sample.Using syringes, this chamber was filled with deionized water and theassembly was heated to 80° C. for 30 minutes after which time the eluatewas removed using a syringe and transferred to a tube.

The spatially encoded constructs were purified by two rounds of positiveselection using magnetic beads to isolate them from any un-encodedprobes, leftover positional-encoding adaptors, or malformed constructs.In the first round of purification, the eluate was hybridized to abiotinylated capture probe comprising a sequence that was complementaryto a sequence spanning the junction of the X positional adaptor (addresstag) and the 5′ end of the joined probe pair. This capture probe wasthen captured on streptavidin functionalized magnetic beads, which werethen washed extensively to remove unbound material. Constructshybridized to capture probes were then eluted by heating in an elutionbuffer containing a blocking oligonucleotide that was complementary tothe capture probe. The eluate was separated from the magnetic beadsusing a magnet, transferred to a new container, and hybridized with abiotinylated capture probe comprising a sequence that was complementaryto a sequence spanning the junction of the 3′ end of the joined probepair and the Y positional adaptor (address tag). This capture probe,together with hybridized constructs, was subsequently captured onstreptavidin functionalized magnetic beads and washed.

The beads were transferred directly into a PCR mix that included primerscomprising sequences that enable sequencing of the PCR products on anIllumina MiSeq instrument. The primers also comprised TruSeq barcodes toallow demultiplexing of multiple samples in a single sequencing run. Afraction of the PCR product was analyzed by gel electrophoresis toverify the presence of the amplified spatially encoded constructs. Theremaining product was purified using a Qiagen PCR purification Kit.Finally, the spatially encoded constructs were purified by sizeselection using either a conventional gel electrophoresis device or thePippen Prep System (Sage Science).

The purified encoded construct was sequenced using an Illumina MiSeqinstrument and the data were used to generate expression maps.

EXAMPLE 6 Spatially Encoded Protein In Situ Assays

This example describes a spatially encoded protein in situ assay. Ahighly multiplexable protein detection assay was carried out on a tissuemicroarray like the ones described supra containing a checkerboardpattern of liver and pancreas tissue cores. In this case a two-plexassay was encoded using a 5-site×5-site addressing scheme. The assay wasperformed by first applying a typical immunostaining procedure with twodifferent primary antibodies, one specific to exocrine cells in thepancreas and one specific to hepatocytes in the liver. Two antibody-DNAconjugates were used as secondary antibodies and were applied to theentire tissue microarray. The conjugates included an oligonucleotidecomprising an identity tag as well as an upstream and downstream splintregion to allow ligation of X and Y address tags. After applying theprimary antibody and secondary antibody conjugate to the entire sampleand washing sufficiently, a pair of microfluidic channel devices wasused to deliver sequentially the X and Y address tags, which wereligated to the oligonucleotide on the conjugate. The conjugates wereeluted from the sample and the combined X and Y tags plus theintervening identity tag formed an amplifiable construct which wasamplified, purified and subjected to next generation sequencing toidentify the abundance of the antibody targets at each spatially encodedlocation.

EXAMPLE 7 Spatially Encoded Protein In Situ Assays

This example describes a spatially encoded protein in situ assay. Asshown in FIG. 6A, a highly multiplexable protein detection assay can becarried out on a sample that preserves the spatial organization of cellsin a tissue, e.g., a paraffin-embedded or fresh-frozen tissue sectionfixed to a glass slide. Assay reagents are protein binders (e.g.antibodies) that are identified via linked DNA tags that can be furtherencoded with tag sequences that encode positional or address information(in this example, indicated as “X” dimension and “Y” dimension). Theaddress tags X and Y are flanked by universal sequences (UP1 and UP2)that can be used as PCR priming sites, adaptors for next-generationsequencing, or both.

As shown in FIG. 6B, the binders, for example, the DNA-labeled antibodyprobes in this example, are delivered over the entire sample surface ina bulk process. The X and Y address tags are then delivered to thesample and coupled to the probes, so that the probes are encoded by theX and Y address tags in a spatially defined pattern. In this example,two sets of tags (i.e., a set of 10 X address tags, namely X1, X2, X3, .. . , X10, and a set of 10 Y address tags, namely Y1, Y2, Y3, . . . ,Y10) are used in a combinatorial fashion, and 100 sites in the samplecan be uniquely identified by the combinations of X and Y address tags.For example, a site in the sample shown in Figure XB is uniquelyidentified as (X9, Y1).

Once the in situ assay is completed, the assay products are eluted andsequenced. The address tag sequence information identifies the site atwhich the assay is performed, and the probe sequence informationidentifies the protein that is targeted. The frequency of a particularassay product in the digital readout can be used to infer the relativeabundance of its target sequence in the sample. This information canthen be associated with other information, including conventionalhistological information, and/or transcript abundance obtained via therelated spatially encoded genomic assay.

EXAMPLE 8 A Method to Reduce Background and Increase Signal-To-NoiseRatio

This example describes a method of detecting rare variant sequences in amixed population of nucleic acids. The method can be integrated into themethods and assay systems disclosed herein, for example, to reduce thebackground contributed by random errors and thus to increase the signalto noise ratio (S/N).

Parallel clonal amplification methods in combination with digitalsequencing have permitted large-scale analysis of variation atresolutions in the range of 1% (Druley et al., 2009, Nat. Methods 6:263-65), but not much below. Although next-generation sequencing enablesde novo discovery and holds great promise for deep analysis of variationacross the genome, a combination of factors at various steps in thesequencing process have made it difficult to obtain very low error ratesat readout. These factors include cross-talk between detection channels,incomplete reactions leading to signal loss, increased background as aresult of loss in synchronicity of nucleotide addition, and noise anderrors in image processing and signal extraction, which worsensignificantly at higher sequencing densities. Thus the sequencingreadout error rate is far above intrinsic rates exhibited by the highfidelity polymerases used in sequencing reactions. For example, an errorrate of 4.4×10⁻⁷ is estimated for Pfusion™ polymerase (New EnglandBiolabs, Ipswich, Mass.). The method described in this example addressesthe above technical issues, by using tags to identify target sequencesthat are “identical by descent.” As illustrated in FIG. 11A, sequencereads can be partitioned into related groups on this basis.

FIG. 11A shows the concept of the rare variant assay, and FIG. 11Bprovides exemplary configurations of probes that can be used tointegrate the rare variant assay in the spatially encoded assays of thepresent disclosure. The top panel of FIG. 11A shows a target sequence ofinterest flanked by adaptors that contain Illumina adaptor sequences forsurface PCR (labeled a and b). The target can be obtained from a varietyof sources, for example, a PCR amplicon. The adaptors contain a variabletag region (labeled z). Both strands are shown to illustrate that theIllumina adaptors are asymmetric. The tagged adaptors are used toconstruct libraries for sequencing. Single molecules are amplified toform “clusters” on the surface of a flowcell. Sequences are determinedfor each target region and its associated tag regions. In the final stepshown, reads are grouped according to their tag regions, based on theassumption that reads with the same tag sequences are identical bydescent, given that z is sufficiently long. The groupings are thenanalyzed to identify rare variant sequences (e.g. targets in the lastset numbered 4 are shown in darker color compared to those in sets 1-3to indicate that the target sequence differs from those in sets 1-3).Similar methods for rare variant sequence detection have been describedin Fu et al., 2011, Proc. Natl. Acad. Sci., 108: 9026-9031, and inSchmitt et al., 2012, Proc. Natl. Acad. Sci., 109: 14508-14513, thedisclosures of which are incorporated by reference herein for allpurposes.

With this strategy, the contribution of random sequencing errors can bevirtually eliminated. Therefore, barring contamination, the ability todetect a rare variant will be limited in theory by the sample size. Notethat although the design shown in FIG. 11A references the Illuminaadaptors and surface amplification methodology, the method is generaland can be used with other sequencing platforms such as the SOLiDplatform (Life Technologies), the 454 platform (Roche), and the PacificBiosciences and Ion Torrent library constructions methods.

A model system was established to quantitate the improvements in thelimit of detection over standard sequencing with the Illumina GAIIxinstrument. The model system consisted of a wild-type 100-mer oligo anda mutant sequence containing a unique, single point mutation in thewild-type sequence. Synthetic oligos were cloned into an E. coli plasmidvector and individual clones were picked and sequence verified in orderto obtain constructs that contained the desired sequences, providingpure, well defined sequence constructs free from oligonucleotidechemical synthesis errors (typically in the range of 0.3-1%). The100-mer of interest was then excised from the plasmid clone byrestriction digestion. Mutant and wild-type oligos were quantitated andmixed at ratios of 1:0, 1:20, 1:1000, 1:10,000, 1:100,000 and1:1,000,000, and 0:1 to simulate the presence of a rare variant in awild-type DNA background.

Next, custom adaptors containing random 10-mer tags were designed andsynthesized. Libraries were prepared from the defined oligo mixtures,and sequenced on an Illumina GAIIx instrument according to theconstructs and steps outlined in FIG. 11A. The data were first analyzedwithout utilizing the tag information (tag z as shown in FIG. 11A). Thisresulted in detection of the point mutation only in the 1:20 sample. Asecond round of analysis utilizing the tags was done using only highquality reads in which tag1/tag2 pairs were retained if the tags weregrouped with each other >99% of the time and had ≥2 replicates. In orderfor a tag group to be scored as a mutation, at least 90% of reads in thegroup had to agree.

The mutant allele was also successfully detected in the 1:10,000,1:100,000, and 1:1,000,000 samples as shown in Table 3. Mutant allelefrequencies within a factor of 2 of the expected value were observed,and this difference was accounted for in dilution and pipetting error.The power to observe a mutation in the wild-type (negative control)sample with ˜7.5 M tag groups is greater than 0.999. Therefore, thedifference between the 1:1,000,000 spiked sample and the negativecontrol was highly significant.

TABLE 3 Demonstration of ability to detect a mutant allele over ~6orders of magnitude Number of Tag Number of Estimated Groups MutantAllele Mutant:WT Assayed Alleles Observed Frequency 1:20 3,433 273 0.081:1,000 2,539 6 0.0024 1:10,000 157,431 26 1.65E−04 1:100,000 1,752,92233 1.88E−05 1:1,000,000 4,186,545 5 1.19E−06 (Negative Ctrl) 1:07,488,853 0 0

The power to observe a mutant with frequency f is 1-(1-f){circumflexover ( )}#tags, so additional sequencing depth can increase thedetection power. The limit of detection in this model system isdetermined only by sample size and any background contamination thatmight be present.

This method can be used to distinguish in vitro amplification errorsfrom rare variants present in the original sample. For example, a simplethreshold that the mutation frequency within a tag group must be >0.9can be used to exclude PCR amplification errors from the analysis. Thisis based on the observation that the expected fraction of copiescontaining an error at that particular location equals 0.5, conditionalon the error occurring in the very first cycle and neglecting the chanceof consecutive PCR errors at the same position. No tags in the negativecontrol pass this criterion.

This method can be integrated into the methods and assay systems fordetermining a spatial pattern of a target abundance, expression, oractivity, in order to reduce the background contributed by random errorsand thus to increase the signal to noise ratio (S/N). Non-limitingexemplary configurations of probes that integrate the X and Y addresstags and the variable tag region z are shown in FIG. 11B.

EXAMPLE 9 Analysis of Brain Tissue

This example describes production of an at least 24-plex protein assaypanel and confirmation of its tissue/cell-type specificity bycorrelation with fluorescent labeling and by analysis of tissuemicroarrays.

A set of 26 antigens is selected. These antigens are expressed inneurons, astrocytes, oligodendrocytes, microglia or proliferating cells,and antibodies that have been raised against the antigens arecommercially available (Table 4). These antibodies have beensuccessfully used, in conjunction with well-established stainingtechniques, to mark different cell types and regions within brainsections (Lyck, et al., 2008, J Histochem Cytochem 56, 201-21). For thepurpose of the assay, it is necessary to avoid procedures for antibodybinding that damage RNA.

Antigen accessibility is addressed by exploring systematically a rangeof “antigen retrieval” protocols and testing their compatibility withRNA. See, Maclntyre, 2001, Br J Biomed Sci. 58,190-6; Kap et al., 2011,PLoS One 6, e27704; Inoue and Wittbrodt, 2011, PLoS One 6, e19713. Apanel of antibody assays rather than any individual assay are exploredto identify a suitable subset for use in a multiplexed panel.

The assay system is also validated by using spatially-encoded andconventional IHC fluorescence data and spatially encoded RNA data,applied to brain tissue. High-dimensional protein and mRNA data from32×32 sites in sections of human brain tissue are generated and comparedwith published data and brain atlas data.

The Allen Brain Atlas (www.brain-map.org) can be used to select targetgenes for production of a panel of gene expression assays with highinformation content, using the methods and assay systems of the presentdisclosure. The “Differential Search” tool is used to interrogate therich spatial expression dataset (generated by in situ hybridization), itis identified that ˜200 genes are present at a range of abundances in atleast one structure/compartment of the brain, and/or are stronglydifferentially expressed between the different structures/compartments.The selection is reviewed to incorporate any new information orcriteria. Probes against the set of ˜200 mRNAs are designed and testedfor their performance in the multiplexed assay, using the online geneexpression data as a reference.

Protein panels and RNA assay panels are applied simultaneously toanalyze sections of normal human brain. For example, the abundance of atleast 24 proteins and 192 mRNA analytes over a 32×32 grid of 50 μmpixels from sections of healthy human brain is analyzed. The results areused to generate a rich map of the brain's spatially-organized molecularterrain, and are amenable to analysis in various ways, including thosethat reveal:

1. The organization of brain into distinct sub-structures: both at theanatomical scale, and at the lower-level multicellular level;

2. Spatial variation in the representation of different cell typesacross the tissue (e.g. using sets of proteins/mRNAs known to bespecific to particular cell types); and

3. The relation between mRNA and protein expression from the same geneat different tissue locations.

TABLE 4 Candidate proteins to differentiate brain tissues, which havebeen used in immunohistochemistry and have commercially availableantibodies. Protein Observed Specificity {Lyck, 2008} b-tubulin IIINeuropil and neuronal bodies CD11b None CD14 Perivascular macrophagesCD34 Endothelium and white blood cells CD39 Endothelium, astroglia, andmacrophages CD45 Microglia, macrophages, and lymphocytes CD68 Microgliaand macrophages CD169 Endothelial and perivascular macrophages CNPaseMyelinated fibers and round cell bodies GFAP Astroglia in white matterand neocortex HLA-DR Microglia/macrophages and lymphocytes Ki-67Perivascular space and sub-ventricular zone MAP-2 Neurons and proximalpart of apical dendrites MBP Myelinated fibers Nestin Endothelialcells/vessel wall NeuN Neuronal cell bodies Neurofilament Neuronal cellprocesses NG2 None Nkx-2.2 None NSE Neuropil O4 sulfatide Myelinatedfibers PDGFa-R None p25a Neuropil and round cell bodies S100b Astrogliain white matter and neocortex TOAD-64 Neuropil Vimentin Astroglia andendothelial cells/vessel wall

All headings are for the convenience of the reader and should not beused to limit the meaning of the text that follows the heading, unlessso specified.

Citation of the above publications or documents is not intended as anadmission that any of them is pertinent prior art, nor does itconstitute any admission as to the contents or date of thesepublications or documents.

While various embodiments of the invention have been described above, itshould be understood that they have been presented by way of exampleonly, and not by way of limitation. Likewise, the various diagrams maydepict an example architectural or other configuration for thedisclosure, which is done to aid in understanding the features andfunctionality that can be included in the disclosure. The disclosure isnot restricted to the illustrated example architectures orconfigurations, but can be implemented using a variety of alternativearchitectures and configurations. Additionally, although the disclosureis described above in terms of various exemplary embodiments andimplementations, it should be understood that the various features andfunctionality described in one or more of the individual embodiments arenot limited in their applicability to the particular embodiment withwhich they are described. They instead can, be applied, alone or in somecombination, to one or more of the other embodiments of the disclosure,whether or not such embodiments are described, and whether or not suchfeatures are presented as being a part of a described embodiment. Thusthe breadth and scope of the present disclosure should not be limited byany of the above-described exemplary embodiments.

We claim:
 1. A method for determining the presence and/or location of agenomic DNA molecule in a biological sample, the method comprising: (a)attaching the biological sample affixed to a support to a firstmicrofluidic device having multiple first addressing channels, wherein afirst addressing channel identifies a first area in the biologicalsample; (b) delivering a first probe through the first addressingchannel to the first area in the biological sample, wherein the firstprobe comprises (i) a first ligation region, (ii) a first address tagthat identifies the first area in the biological sample, and (iii) asecond ligation region; (c) attaching the biological sample affixed tothe support to a second microfluidic device having multiple secondaddressing channels, wherein a second addressing channel identifies asecond area in the biological sample that intersects with the firstarea; and (d) delivering a second probe through the second addressingchannel to the second area in the biological sample, wherein the secondprobe comprises: (i) a second address tag that identifies the secondarea in the biological sample and (ii) a third ligation region, whereinthe second probe is coupled to the first probe through ligation betweenthe second ligation region and the third ligation region at anintersection between the first area and the second area, therebygenerating a ligation product, and the first and second address tags areused to identify the presence and/or the location of the genomic DNAmolecule at the intersection in the biological sample.
 2. The method ofclaim 1, wherein the multiple first addressing channels aresubstantially parallel to each other and the multiple second addressingchannels are substantially parallel to each other.
 3. The method ofclaim 1, wherein the multiple first addressing channels and/or themultiple second addressing channels is n addressing channels, wherein nis an integer between 20 and
 1000. 4. The method of claim 3, wherein nis about
 50. 5. The method of claim 1, wherein the width of each of themultiple first addressing channels and/or each of the multiple secondaddressing channels is about 1 micrometers (μm) to about 500 μm.
 6. Themethod of claim 1, wherein the depth of each of the multiple firstaddressing channels and/or each of the multiple second addressingchannels is about 1 μm to about 500 μm.
 7. The method of claim 1,wherein the distance between each of the multiple first addressingchannels and/or between each of the multiple second addressing channelsis about 1 μm to about 2.0 millimeters (mm).
 8. The method of claim 1,wherein the second area forms an angle with the first area at theintersection, and wherein the angle is about 10 degrees to about 90degrees.
 9. The method of claim 8, wherein the angle is about 90degrees.
 10. The method of claim 1, further comprising attachingadaptors to each end of the genomic DNA molecule, wherein at least oneof the adaptors comprises a fourth ligation region.
 11. The method ofclaim 10, wherein the first probe is coupled to the genomic DNA moleculethrough ligation between the first ligation region and the fourthligation region.
 12. The method of claim 11, further comprisingextending the first probe using the genomic DNA molecule as a template.13. The method of claim 1, wherein the second probe is coupled with thethird probe by extension followed by ligation.
 14. The method of claim10, wherein the first probe is coupled to one of the adaptors throughligation between the first ligation region and the fourth ligationregion.
 15. The method of claim 1, wherein the first probe furthercomprises a variable tag region, a primer sequence, a sequencingadaptor, a biotin moiety, or a combination thereof.
 16. The method ofclaim 1, wherein the second probe further comprises a variable tagregion, a primer sequence, a sequencing adaptor, a biotin moiety, or acombination thereof.
 17. The method of claim 1, wherein the third probefurther comprises a variable tag region, a sequencing adaptor, or acombination thereof.
 18. The method of claim 1, wherein the first probe,the second probe, and/or the third probe comprises DNA.
 19. The methodof claim 1, wherein the genomic DNA molecule in the biological samplecomprises accessible genomic DNA.
 20. The method of claim 1, furthercomprising amplifying the ligation product.
 21. The method of claim 20,wherein the amplifying is performed by polymerase chain reaction. 22.The method of claim 1, wherein the method further comprises determiningthe sequence of the first and second address tags by nucleic acidsequencing or high-throughput sequencing.
 23. The method of claim 1,further comprising, prior to step (a), staining the biological sampleusing immunohistochemistry or immunofluorescence.
 24. The method ofclaim 23, further comprising imaging the biological sample.
 25. Themethod of claim 1, further comprising imaging the biological sample. 26.The method of claim 1, wherein the method determines the presence andlocation of the genomic DNA molecule in the biological sample.
 27. Themethod of claim 1, wherein the biological sample is a fixed tissuesample, a fresh frozen tissue sample, an embedded tissue sample, or aprocessed tissue sample.
 28. The method of claim 27, wherein the fixedtissue sample is a formalin-fixed, paraffin-embedded (FFPE) sample. 29.The method of claim 1, further comprising determining the presenceand/or location of additional genomic DNA molecules in the biologicalsample, wherein the one or more additional genomic DNA molecules is aninteger between 1,000 and 100,000.